| ▼ symlinks | |
| ▼ rosetta | |
| ▼ src | |
| ► protocols | |
| ► abinitio | |
| ► abscript | |
| AbscriptLoopCloserCM.cc | |
| AbscriptLoopCloserCM.fwd.hh | Definition of the AbscriptLoopCloserCM class |
| AbscriptLoopCloserCM.hh | |
| AbscriptMover.cc | |
| AbscriptMover.fwd.hh | Definition of the AbscriptMover class |
| AbscriptMover.hh | |
| AbscriptMoverCreator.hh | This class will create instances of Mover AbscriptMover for the MoverFactory |
| AbscriptStageMover.cc | |
| AbscriptStageMover.fwd.hh | Definition of the AbscriptStageMover class |
| AbscriptStageMover.hh | |
| ConstraintPreparer.cc | |
| ConstraintPreparer.fwd.hh | Definition of the ConstraintPreparer class |
| ConstraintPreparer.hh | |
| ConstraintPreparerCreator.hh | This class will create instances of Mover ConstraintPreparer for the MoverFactory |
| FragmentCM.cc | |
| FragmentCM.fwd.hh | Definition of the FragmentCM class |
| FragmentCM.hh | |
| FragmentJumpCM.cc | |
| FragmentJumpCM.fwd.hh | Definition of the FragmentJumpCM class |
| FragmentJumpCM.hh | |
| FragmentJumpCMCreator.hh | This class will create instances of Mover AbscriptMover for the MoverFactory |
| JumpSampleData.cc | |
| JumpSampleData.fwd.hh | Definition of the JumpSampleData class |
| JumpSampleData.hh | |
| JumpSampleDataCreator.hh | This class will create instances of Mover AbscriptMover for the MoverFactory |
| StageID.hh | |
| StagePreparer.cc | |
| StagePreparer.fwd.hh | Definition of the StagePreparer class |
| StagePreparer.hh | |
| AbrelaxApplication.cc | |
| AbrelaxApplication.hh | |
| AbrelaxMover.cc | This class will be handled to a SampleProtocol as a control instance |
| AbrelaxMover.fwd.hh | |
| AbrelaxMover.hh | |
| AllResiduesChanged.hh | |
| BrokerMain.cc | |
| BrokerMain.hh | |
| ClassicAbinitio.cc | Ab-initio fragment assembly protocol for proteins |
| ClassicAbinitio.fwd.hh | |
| ClassicAbinitio.hh | Header file for ClassicAbinitio protocol |
| ConstraintFragmentSampler.cc | Ab-initio fragment assembly protocol for proteins |
| ConstraintFragmentSampler.hh | Header file for ConstraintFragmentSampler protocol |
| DomainAssembly.cc | |
| DomainAssembly.hh | |
| DomainAssemblyCreator.hh | Declaration of the MoverCreator class for the DomainAssembly |
| DoubleLayerKinematicAbinitio.cc | |
| DoubleLayerKinematicAbinitio.fwd.hh | |
| DoubleLayerKinematicAbinitio.hh | |
| FoldConstraints.cc | Ab-initio fragment assembly protocol for proteins under the influence of contraints (e.g., NOE) |
| FoldConstraints.fwd.hh | |
| FoldConstraints.hh | Abinitio-Folding under (distance-)constraints |
| FragmentCost.hh | |
| FragmentSampler.cc | Ab-initio fragment assembly protocol for proteins |
| FragmentSampler.fwd.hh | |
| FragmentSampler.hh | Header file for FragmentSampler protocol |
| HedgeArchive.cc | |
| HedgeArchive.fwd.hh | |
| HedgeArchive.hh | |
| IterativeAbrelax.cc | |
| IterativeAbrelax.hh | |
| IterativeBase.cc | |
| IterativeBase.hh | |
| IterativeCentroid.cc | |
| IterativeCentroid.hh | |
| IterativeFullatom.cc | |
| IterativeFullatom.hh | |
| JumpingFoldConstraints.hh | |
| KinematicAbinitio.cc | |
| KinematicAbinitio.fwd.hh | |
| KinematicAbinitio.hh | Abinitio - Type sampling controlled by KinematicControl object |
| KinematicControl.cc | |
| KinematicControl.fwd.hh | |
| KinematicControl.hh | |
| KinematicTaskControl.cc | |
| KinematicTaskControl.fwd.hh | |
| KinematicTaskControl.hh | |
| LoopJumpFoldCst.cc | |
| LoopJumpFoldCst.fwd.hh | |
| LoopJumpFoldCst.hh | |
| MembraneAbinitio.cc | Ab-initio fragment assembly protocol for membrane proteins |
| MembraneAbinitio.fwd.hh | |
| MembraneAbinitio.hh | Header file for MembraneAbinitio protocol |
| PairingStatistics.cc | |
| PairingStatistics.fwd.hh | |
| PairingStatistics.hh | |
| Protocol.cc | |
| Protocol.fwd.hh | |
| Protocol.hh | |
| ResolutionSwitcher.cc | |
| ResolutionSwitcher.fwd.hh | |
| ResolutionSwitcher.hh | |
| StrandConstraints.cc | |
| StrandConstraints.hh | |
| Template.cc | |
| Template.fwd.hh | |
| Template.hh | |
| TemplateJumpSetup.cc | |
| TemplateJumpSetup.fwd.hh | |
| TemplateJumpSetup.hh | |
| Templates.cc | |
| Templates.fwd.hh | |
| Templates.hh | |
| vs_test.cc | |
| vs_test.hh | |
| ► analysis | |
| InterfaceAnalyzerMover.cc | InterfaceAnalyzerMover implementation - class for in-depth interface quality analysis |
| InterfaceAnalyzerMover.fwd.hh | Fwd declaration for InterfaceAnalyzer: intense analysis of interface quality |
| InterfaceAnalyzerMover.hh | |
| InterfaceAnalyzerMoverCreator.hh | This class will create instances of Mover InterfaceAnalyzerMover for the MoverFactory |
| LoopAnalyzerMover.cc | LoopAnalyzerMover implementation - class for in-depth loop structure quality analysis |
| LoopAnalyzerMover.fwd.hh | Fwd declaration for LoopAnalyzer: intense analysis of loop quality |
| LoopAnalyzerMover.hh | LoopAnalyzerMover examines loop structures and packages extra scores into a Job object |
| PackStatMover.cc | |
| PackStatMover.fwd.hh | Created on: Jan 25, 2012 |
| PackStatMover.hh | |
| ► anchored_design | |
| Anchor.cc | |
| Anchor.fwd.hh | |
| Anchor.hh | |
| AnchorMovers.cc | -*- mode:c++;tab-width:2;indent-tabs-mode:t;show-trailing-whitespace:t;rm-trailing-spaces:t -*- |
| AnchorMovers.fwd.hh | Anchor Movers forward declarations header |
| AnchorMovers.hh | Protocol-level outermost movers for anchored design; wraps a set of other moves |
| AnchorMoversData.cc | |
| AnchorMoversData.fwd.hh | |
| AnchorMoversData.hh | |
| ► antibody | |
| ► clusters | |
| CDRCluster.cc | Simple class to hold and access CDRCluster information of a region in a pose |
| CDRCluster.fwd.hh | |
| CDRCluster.hh | Simple class to hold and access CDRcluster info at a region in the pose. Construct in CDRClusterSet |
| CDRClusterEnum.hh | Enumerators for antibody clusters |
| CDRClusterEnumManager.cc | |
| CDRClusterEnumManager.fwd.hh | |
| CDRClusterEnumManager.hh | Functions for CDRClusterEnums |
| CDRClusterFeatures.cc | |
| CDRClusterFeatures.fwd.hh | |
| CDRClusterFeatures.hh | |
| CDRClusterFeaturesCreator.cc | |
| CDRClusterFeaturesCreator.hh | |
| CDRClusterMatcher.cc | Simple class for identifying CDR cluster in an antibody |
| CDRClusterMatcher.fwd.hh | |
| CDRClusterMatcher.hh | Simple class for identifying CDR cluster of an antibody |
| CDRClusterSet.cc | |
| CDRClusterSet.fwd.hh | |
| CDRClusterSet.hh | |
| util.cc | |
| util.hh | |
| ► design | |
| AntibodyCDRDesigner.cc | |
| AntibodyCDRDesigner.fwd.hh | |
| AntibodyCDRDesigner.hh | |
| AntibodyDatabaseManager.cc | Handles all loading of CDR, Framework, and cluster/dmap info from external database file |
| AntibodyDatabaseManager.fwd.hh | Handles all loading of CDR, Framework, and cluster/dmap info from database file |
| AntibodyDatabaseManager.hh | Handles all loading of CDR, Framework, and cluster/dmap info from external database file |
| AntibodyDesignEnum.hh | Antibody Design enumerators |
| AntibodyDesignModeler.cc | |
| AntibodyDesignModeler.fwd.hh | |
| AntibodyDesignModeler.hh | |
| AntibodyDesignMover.cc | Handles the Antibody Design Protocol |
| AntibodyDesignMover.fwd.hh | Handles all loading of CDR, Framework, and cluster/dmap info from database file |
| AntibodyDesignMover.hh | Handles the Antibody Design Protocol |
| AntibodyGraftDesigner.cc | Class that initially designs antibodies through grafting using an AntibodyDatabase + North_AHO numbering scheme |
| AntibodyGraftDesigner.fwd.hh | |
| AntibodyGraftDesigner.hh | Class that initially designs antibodies through grafting using an AntibodyDatabase + North_AHO numbering scheme |
| ConservativeDesignOperation.cc | |
| ConservativeDesignOperation.fwd.hh | |
| ConservativeDesignOperation.hh | TaskOperation to allow only conservative mutations at designable residues |
| ConservativeDesignOperationCreator.hh | |
| DesignInstructionsParser.cc | |
| DesignInstructionsParser.hh | Parsers Antibody Design Instruction files |
| ResidueProbDesignOperation.cc | |
| ResidueProbDesignOperation.fwd.hh | |
| ResidueProbDesignOperation.hh | Uses a probability distribution to sample allowed residues at a position, adding those types to the packer - only if they are designable |
| ResidueProbDesignOperationCreator.hh | |
| util.cc | |
| util.hh | Utility functions for antibody design namespace |
| ► snugdock | |
| SnugDock.cc | |
| SnugDock.fwd.hh | Forward declaration |
| SnugDock.hh | |
| SnugDockProtocol.cc | |
| SnugDockProtocol.fwd.hh | Forward declaration |
| SnugDockProtocol.hh | |
| Ab_TemplateInfo.cc | |
| Ab_TemplateInfo.fwd.hh | |
| Ab_TemplateInfo.hh | |
| AntibodyEnum.hh | Enumerators + TypeDefs for Antibody namespace |
| AntibodyEnumManager.cc | Functions for AntibodyEnumerators |
| AntibodyEnumManager.fwd.hh | |
| AntibodyEnumManager.hh | Functions for AntibodyEnumerators |
| AntibodyInfo.cc | Class for getting antibody-specific objects and information |
| AntibodyInfo.fwd.hh | AntibodyInfo class forward declarations header |
| AntibodyInfo.hh | Class for getting antibody-specific objects and information |
| AntibodyModelerProtocol.cc | Build a homology model of an antibody |
| AntibodyModelerProtocol.fwd.hh | Forward declaration |
| AntibodyModelerProtocol.hh | Build a homology model of an antibody |
| AntibodyNumberingParser.cc | |
| AntibodyNumberingParser.fwd.hh | |
| AntibodyNumberingParser.hh | Read Antibody Numbering schemes and transform info from the database |
| CDRsMinPackMin.cc | Build a homology model of an antibody |
| CDRsMinPackMin.fwd.hh | Forward declaration |
| CDRsMinPackMin.hh | Main CDR minimization method in protocols/antibody |
| CloseOneCDRLoop.cc | Grafts a cdr onto the template of an antibody framework |
| CloseOneCDRLoop.fwd.hh | |
| CloseOneCDRLoop.hh | |
| GraftCDRLoopsProtocol.cc | Build a homology model of an antibody |
| GraftCDRLoopsProtocol.fwd.hh | Forward declaration |
| GraftCDRLoopsProtocol.hh | Build a homology model of an antibody |
| GraftedStemOptimizer.cc | Optimize the CDR Grafted stem |
| GraftedStemOptimizer.fwd.hh | |
| GraftedStemOptimizer.hh | Optimize the CDR Grafted stem |
| GraftOneCDRLoop.cc | Grafts a cdr onto the template of an antibody framework |
| GraftOneCDRLoop.fwd.hh | |
| GraftOneCDRLoop.hh | Grafts a cdr onto the template of an antibody framework |
| H3CterInsert.cc | Build a homology model of an antibody |
| H3CterInsert.fwd.hh | Build a homology model of an antibody |
| H3CterInsert.hh | Build a homology model of an antibody |
| H3PerturbCCD.cc | Build a homology model of an antibody |
| H3PerturbCCD.fwd.hh | |
| H3PerturbCCD.hh | Build a homology model of an antibody |
| H3RefineCCD.cc | Build a homology model of an antibody |
| H3RefineCCD.fwd.hh | |
| H3RefineCCD.hh | Build a homology model of an antibody |
| LHRepulsiveRamp.cc | Build a homology model of an antibody |
| LHRepulsiveRamp.fwd.hh | |
| LHRepulsiveRamp.hh | Build a homology model of an antibody |
| metrics.cc | Routines to measure antibodies |
| metrics.hh | |
| ModelCDRH3.cc | Models CDR H3 loop using loop modeling |
| ModelCDRH3.fwd.hh | |
| ModelCDRH3.hh | |
| RefineBetaBarrel.cc | Build a homology model of an antibody |
| RefineBetaBarrel.fwd.hh | Forward declaration |
| RefineBetaBarrel.hh | Build a homology model of an antibody |
| RefineOneCDRLoop.cc | Build a homology model of an antibody |
| RefineOneCDRLoop.fwd.hh | |
| RefineOneCDRLoop.hh | Build a homology model of an antibody |
| RefineOneCDRLoopCentroid.cc | Build a homology model of an antibody |
| RefineOneCDRLoopCentroid.fwd.hh | |
| RefineOneCDRLoopCentroid.hh | Build a homology model of an antibody |
| util.cc | |
| util.hh | Utility functions for the Antibody namespace |
| ► antibody_legacy | |
| AntibodyClass.cc | |
| AntibodyClass.fwd.hh | Antibody class forward declarations header |
| AntibodyClass.hh | |
| AntibodyModeler.cc | |
| AntibodyModeler.fwd.hh | Forward declaration |
| AntibodyModeler.hh | |
| CDRH3Modeler.cc | Models CDR H3 loop using loop modeling |
| CDRH3Modeler.hh | |
| GraftMover.cc | |
| GraftMover.hh | |
| LHRepulsiveRampLegacy.cc | |
| LHRepulsiveRampLegacy.fwd.hh | |
| LHRepulsiveRampLegacy.hh | |
| LHSnugFitLegacy.cc | |
| LHSnugFitLegacy.fwd.hh | |
| LHSnugFitLegacy.hh | |
| Ubiquitin_E2C_Modeler.cc | |
| Ubiquitin_E2C_Modeler.fwd.hh | Forward declaration |
| Ubiquitin_E2C_Modeler.hh | Build model for di-ubiquitin and e2c enzyme complex |
| ► backrub | |
| BackrubMover.cc | Implementation of BackrubMover class and functions |
| BackrubMover.fwd.hh | |
| BackrubMover.hh | Definition of BackrubMover class and functions |
| BackrubMoverCreator.hh | This class will create instances of Mover BackrubMover for the MoverFactory |
| BackrubSegment.cc | Implmentation of BackrubSegment class |
| BackrubSegment.hh | Definition/implmentation of BackrubSegment class |
| BackrubSidechainMover.cc | BackrubSidechainMover methods implemented |
| BackrubSidechainMover.fwd.hh | BackrubSidechainMover forward declarations header |
| BackrubSidechainMover.hh | |
| BackrubSidechainMoverCreator.hh | This class will create instances of Mover BackrubSidechainMover for the MoverFactory |
| ► boinc | |
| boinc.cc | Wrappers to make BOINC work |
| boinc.hh | Wrappers to make BOINC work |
| boinc_shmem.hh | |
| BoincPoseObserver.cc | BoincPoseObserver class |
| BoincPoseObserver.fwd.hh | |
| BoincPoseObserver.hh | BoincPoseObserver class |
| util.cc | |
| util.hh | |
| watchdog.cc | |
| watchdog.hh | |
| ► branch_angle | |
| BranchAngleOptimizer.cc | |
| BranchAngleOptimizer.fwd.hh | BranchAngleOptimizer class forward declaration |
| BranchAngleOptimizer.hh | |
| BranchCoef1.fwd.hh | BranchCoef1 class forward declaration |
| BranchCoef1.hh | Definition/implementation of BranchCoef1 class and methods |
| BranchCoef2.fwd.hh | BranchCoef2 class forward declaration |
| BranchCoef2.hh | Definition/implementation of BranchCoef2 class and methods |
| BranchParam1.fwd.hh | BranchParam1 class forward declaration |
| BranchParam1.hh | Definition/implementation of BranchParam1 class and methods |
| BranchParam2.fwd.hh | BranchParam2 class forward declaration |
| BranchParam2.hh | Definition/implementation of BranchParam2 class and methods |
| ► canonical_sampling | |
| ► mc_convergence_checks | |
| Heat_ConvergenceCheck.hh | |
| HierarchicalLevel.cc | |
| HierarchicalLevel.fwd.hh | |
| HierarchicalLevel.hh | |
| HPool.cc | Hierarchical pool |
| HPool.fwd.hh | Hierarchical pool |
| HPool.hh | Hierarchical pool |
| MPIBPool_ConvergenceCheck.cc | |
| MPIBPool_ConvergenceCheck.fwd.hh | |
| MPIBPool_ConvergenceCheck.hh | |
| MPIHPool_ConvergenceCheck.cc | |
| MPIHPool_ConvergenceCheck.fwd.hh | |
| MPIHPool_ConvergenceCheck.hh | |
| MPIPool_ConvergenceCheck.cc | |
| MPIPool_ConvergenceCheck.fwd.hh | |
| MPIPool_ConvergenceCheck.hh | |
| Pool_ConvergenceCheck.cc | |
| Pool_ConvergenceCheck.hh | |
| pool_util.cc | |
| pool_util.hh | |
| util.cc | |
| util.hh | |
| CanonicalSamplingApplication.cc | |
| CanonicalSamplingApplication.hh | |
| CanonicalSamplingMover.cc | |
| CanonicalSamplingMover.fwd.hh | |
| CanonicalSamplingMover.hh | |
| DbTrajectoryReader.cc | |
| DbTrajectoryReader.fwd.hh | |
| DbTrajectoryReader.hh | |
| DbTrajectoryRecorder.cc | |
| DbTrajectoryRecorder.fwd.hh | |
| DbTrajectoryRecorder.hh | |
| DbTrajectoryRecorderCreator.hh | This class will create instances of Mover DbTrajectoryRecorder for the MoverFactory |
| FixedTemperatureController.cc | |
| FixedTemperatureController.fwd.hh | |
| FixedTemperatureController.hh | |
| MetricRecorder.cc | |
| MetricRecorder.fwd.hh | Forward declarations for class MetricRecorder |
| MetricRecorder.hh | |
| MetricRecorderCreator.hh | This class will create instances of Mover MetricRecorder for the MoverFactory |
| MetropolisHastingsMover.cc | MetropolisHastingsMover methods implemented |
| MetropolisHastingsMover.fwd.hh | MetropolisHastingsMover forward declarations header |
| MetropolisHastingsMover.hh | Implement replica exchange in the MetropolisHastingsMover Framework |
| MetropolisHastingsMoverCreator.hh | This class will create instances of Mover MetropolisHastingsMover for the MoverFactory |
| MpiHamiltonianExchange.cc | |
| MpiHamiltonianExchange.fwd.hh | |
| MpiHamiltonianExchange.hh | |
| MpiHamiltonianExchangeCreator.hh | This class will create instances of Mover MpiHamiltonianExchange for the MoverFactory |
| MpiParallelTempering.cc | |
| MpiParallelTempering.fwd.hh | |
| MpiParallelTempering.hh | |
| MpiParallelTemperingCreator.hh | This class will create instances of Mover MpiParallelTempering for the MoverFactory |
| MultiTempTrialCounter.cc | MultiTempTrialCounter methods implemented |
| MultiTempTrialCounter.fwd.hh | |
| MultiTempTrialCounter.hh | |
| PDBTrajectoryRecorder.cc | |
| PDBTrajectoryRecorder.fwd.hh | |
| PDBTrajectoryRecorder.hh | |
| PDBTrajectoryRecorderCreator.hh | This class will create instances of Mover PDBTrajectoryRecorder for the MoverFactory |
| ProgressBarObserver.cc | |
| ProgressBarObserver.fwd.hh | |
| ProgressBarObserver.hh | |
| ProgressBarObserverCreator.hh | |
| readme.hh | |
| SidechainMetropolisHastingsMover.cc | SidechainMetropolisHastingsMover methods implemented |
| SidechainMetropolisHastingsMover.fwd.hh | |
| SidechainMetropolisHastingsMover.hh | |
| SidechainMetropolisHastingsMoverCreator.hh | This class will create instances of Mover SidechainMetropolisHastingsMover for the MoverFactory |
| SilentTrajectoryRecorder.cc | |
| SilentTrajectoryRecorder.fwd.hh | Forward declarations for class SilentTrajectoryRecorder |
| SilentTrajectoryRecorder.hh | |
| SilentTrajectoryRecorderCreator.hh | This class will create instances of Mover SilentTrajectoryRecorder for the MoverFactory |
| SimulatedTempering.cc | |
| SimulatedTempering.fwd.hh | |
| SimulatedTempering.hh | |
| SimulatedTemperingCreator.hh | This class will create instances of Mover SimulatedTempering for the MoverFactory |
| SimulatedTemperingObserver.fwd.hh | |
| TemperatureController.cc | |
| TemperatureController.fwd.hh | |
| TemperatureController.hh | |
| ThermodynamicMover.cc | ThermodynamicMover methods implemented |
| ThermodynamicMover.fwd.hh | ThermodynamicMover forward declarations header |
| ThermodynamicMover.hh | |
| ThermodynamicObserver.cc | ThermodynamicObserver methods implemented |
| ThermodynamicObserver.fwd.hh | ThermodynamicObserver forward declarations header |
| ThermodynamicObserver.hh | |
| TrajectoryRecorder.cc | |
| TrajectoryRecorder.fwd.hh | Forward declarations for class TrajectoryRecorder |
| TrajectoryRecorder.hh | |
| ► cartesian | |
| md.cc | |
| md.hh | |
| ► checkpoint | |
| Checkpoint.cc | |
| Checkpoint.fwd.hh | |
| Checkpoint.hh | |
| CheckPointer.cc | |
| CheckPointer.fwd.hh | |
| CheckPointer.hh | |
| ► cluster | |
| APCluster.cc | |
| APCluster.fwd.hh | |
| APCluster.hh | |
| cluster.cc | |
| cluster.hh | |
| ► coarse_rna | |
| CoarseRNA_DeNovoProtocol.cc | |
| CoarseRNA_DeNovoProtocol.hh | |
| CoarseRNA_Fragments.cc | |
| CoarseRNA_Fragments.hh | |
| CoarseRNA_LoopCloser.cc | |
| CoarseRNA_LoopCloser.fwd.hh | |
| CoarseRNA_LoopCloser.hh | |
| ► comparative_modeling | |
| ► features | |
| ResidueFeature.cc | |
| ResidueFeature.fwd.hh | Forward declaration for ResidueFeature class |
| ResidueFeature.hh | Abstract base class for per-residue features used in comparative modeling |
| ResidueFeatureFactory.cc | Factory for creating various types of ResidueFeatures |
| ResidueFeatureFactory.hh | |
| SSFeature.cc | |
| SSFeature.fwd.hh | Forward declaration for SSFeature class |
| SSFeature.hh | |
| TorsionFeature.cc | |
| TorsionFeature.fwd.hh | Forward declaration for TorsionFeature class |
| TorsionFeature.hh | |
| Align_RmsdEvaluator.cc | |
| Align_RmsdEvaluator.fwd.hh | Forward declaration for Align_RmsdEvaluator class |
| Align_RmsdEvaluator.hh | |
| Align_RotamerEvaluator.cc | |
| Align_RotamerEvaluator.fwd.hh | Forward declaration for Align_RotamerEvaluator class |
| Align_RotamerEvaluator.hh | |
| AlignmentClustering.cc | |
| AlignmentClustering.fwd.hh | |
| AlignmentClustering.hh | Divide input alns into clusters based on gdtmm comparison of partial models. Uses the top e-value or hh-value sample as the cluster center |
| AlignmentID.hh | |
| AlignmentSet.cc | |
| AlignmentSet.fwd.hh | Forward declaration for AlignmentSet class |
| AlignmentSet.hh | |
| AlignRmsdTargetEvaluatorCreator.cc | |
| AlignRmsdTargetEvaluatorCreator.hh | Header for AlignRmsdTargetEvaluatorCreator |
| cm_main.cc | |
| cm_main.hh | |
| coord_util.cc | |
| coord_util.hh | |
| ExtraThreadingMover.cc | Method declarations for ExtraThreadingMover |
| ExtraThreadingMover.hh | Class for copying extra stuff (ligands,dna,peptides,etc) from a template Pose |
| GenericJobInputter.cc | |
| GenericJobInputter.fwd.hh | Header file for ThreadingJobInputter class, part of August 2008 job distributor as planned at RosettaCon08 |
| GenericJobInputter.hh | |
| GenericJobInputterCreator.hh | |
| IgnoreSubsetConstraintSet.cc | |
| IgnoreSubsetConstraintSet.fwd.hh | Forward declaration for IgnoreSubsetConstraintSet class |
| IgnoreSubsetConstraintSet.hh | |
| LoopRelaxMover.cc | |
| LoopRelaxMover.fwd.hh | Forward declaration for LoopRelaxMover class |
| LoopRelaxMover.hh | |
| LoopRelaxMoverCreator.hh | |
| LoopRelaxThreadingMover.cc | |
| LoopRelaxThreadingMover.fwd.hh | Forward declaration for LoopRelaxThreadingMover class |
| LoopRelaxThreadingMover.hh | |
| MultiThreadingMover.cc | |
| MultiThreadingMover.hh | |
| PartialThreadingMover.cc | |
| PartialThreadingMover.hh | |
| RecoverSideChainsMover.cc | |
| RecoverSideChainsMover.fwd.hh | Forward declaration for RecoverSideChainsMover class |
| RecoverSideChainsMover.hh | |
| StealLigandMover.cc | |
| StealLigandMover.fwd.hh | Forward declaration for StealLigandMover class |
| StealLigandMover.hh | |
| StealSideChainsMover.cc | |
| StealSideChainsMover.fwd.hh | Forward declaration for StealSideChainsMover class |
| StealSideChainsMover.hh | |
| ThreadingJob.cc | |
| ThreadingJob.fwd.hh | Header file for ThreadingJob classes |
| ThreadingJob.hh | Header file for ThreadingJob classes |
| ThreadingJobInputter.cc | |
| ThreadingJobInputter.fwd.hh | |
| ThreadingJobInputter.hh | |
| ThreadingJobInputterCreator.hh | |
| ThreadingMover.cc | Method declarations for ThreadingMover |
| ThreadingMover.hh | |
| util.cc | Set of utilities used in comparative modeling of protein structures |
| util.hh | Small bundle of utilities for comparative modeling |
| ► constraints_additional | |
| AdditionalConstraintCreators.cc | |
| AdditionalConstraintCreators.hh | |
| AmbiguousMultiConstraint.cc | Declarations for a type of constraint that holds a number of constraints |
| AmbiguousMultiConstraint.fwd.hh | |
| AmbiguousMultiConstraint.hh | Declarations for a type of constraint that holds multiple other |
| BindingSiteConstraint.cc | |
| BindingSiteConstraint.hh | |
| CombinedConstraintEvaluator.cc | |
| CombinedConstraintEvaluator.hh | |
| CombinedConstraintEvaluatorCreator.cc | |
| CombinedConstraintEvaluatorCreator.hh | |
| COMCoordinateConstraint.cc | |
| COMCoordinateConstraint.hh | |
| ConstraintEvaluator.cc | |
| ConstraintEvaluator.fwd.hh | |
| ConstraintEvaluator.hh | |
| ConstraintEvaluatorCreator.cc | |
| ConstraintEvaluatorCreator.hh | |
| MaxSeqSepConstraintSet.cc | |
| MaxSeqSepConstraintSet.fwd.hh | |
| MaxSeqSepConstraintSet.hh | Helper class for FoldConstraints Protocol, filters constraints by sequence separation |
| SequenceCoupling1BDConstraint.cc | |
| SequenceCoupling1BDConstraint.fwd.hh | This is a constraint that refers to a core::sequence::SequenceCoupling? in order to influence the scoring of amino acid types based on multiple sequence alignments (i.e. for biasing amino acid choices during design) |
| SequenceCoupling1BDConstraint.hh | This is a constraint that refers to a core::sequence::SequenceCoupling1BD? in order to influence the scoring of amino acid types based on multiple sequence alignments (i.e. for biasing amino acid choices during design) |
| SequenceCouplingConstraint.cc | |
| SequenceCouplingConstraint.fwd.hh | This is a constraint that refers to a core::sequence::SequenceCoupling? in order to influence the scoring of amino acid types based on multiple sequence alignments (i.e. for biasing amino acid choices during design) |
| SequenceCouplingConstraint.hh | This is a constraint that refers to a core::sequence::SequenceCoupling? in order to influence the scoring of amino acid types based on multiple sequence alignments (i.e. for biasing amino acid choices during design) |
| ► contact_map | |
| ContactMap.cc | Method code and full headers for ContactMapCreator, ContactMap, ContactPartner and contact |
| ContactMap.fwd.hh | |
| ContactMap.hh | Mover to create a ContactMap |
| ContactMapCreator.hh | |
| ► cryst | |
| cryst_movers.cc | Protocols for folding into density |
| cryst_movers.hh | |
| cryst_movers_creator.hh | |
| ► ddg | |
| ddG_main.cc | |
| ddG_main.hh | |
| ddGData.cc | |
| ddGData.fwd.hh | |
| ddGData.hh | |
| ddGMover.cc | |
| ddGMover.hh | |
| ► denovo_design | |
| ► filters | |
| ExposedHydrophobicsFilter.cc | Tom's Denovo design protocol |
| ExposedHydrophobicsFilter.fwd.hh | Fwd declarations for Tom's denovo design protocol |
| ExposedHydrophobicsFilter.hh | Tom's Denovo Protocol. This is freely mutable and used for playing around with stuff |
| ExposedHydrophobicsFilterCreator.hh | |
| ► design_opt | |
| GreedyOptMutationMover.cc | |
| GreedyOptMutationMover.fwd.hh | |
| GreedyOptMutationMover.hh | |
| GreedyOptMutationMoverCreator.hh | |
| ParetoOptMutationMover.cc | |
| ParetoOptMutationMover.fwd.hh | |
| ParetoOptMutationMover.hh | |
| ParetoOptMutationMoverCreator.hh | This class will create instances of Mover ParetoOptMutationMover for the MoverFactory |
| PointMutationCalculator.cc | |
| PointMutationCalculator.fwd.hh | |
| PointMutationCalculator.hh | |
| ► dna | |
| DesignProteinBackboneAroundDNA.cc | Performs a round flexible backbone sampling/design. (Interim(?) encapsulation of some loose code in a mover class.) |
| DesignProteinBackboneAroundDNA.fwd.hh | |
| DesignProteinBackboneAroundDNA.hh | Performs a round flexible backbone sampling/design. (Interim(?) encapsulation of some loose code in a mover class.) |
| DesignProteinBackboneAroundDNACreator.hh | |
| DnaChains.cc | |
| DnaChains.fwd.hh | |
| DnaChains.hh | Descriptive but lightweight class to keep track of (usually basepaired) dna chains |
| DnaDesignDef.cc | |
| DnaDesignDef.fwd.hh | |
| DnaDesignDef.hh | |
| DnaInterfaceFinder.cc | |
| DnaInterfaceFinder.fwd.hh | |
| DnaInterfaceFinder.hh | |
| DnaInterfaceMinMover.cc | |
| DnaInterfaceMinMover.fwd.hh | |
| DnaInterfaceMinMover.hh | A mover that minimizes protein residues near DNA |
| DnaInterfaceMinMoverCreator.hh | |
| DnaInterfaceMultiStateDesign.cc | |
| DnaInterfaceMultiStateDesign.fwd.hh | |
| DnaInterfaceMultiStateDesign.hh | |
| DnaInterfaceMultiStateDesignCreator.hh | |
| DnaInterfacePacker.cc | |
| DnaInterfacePacker.fwd.hh | |
| DnaInterfacePacker.hh | Intended to perform anything one would want to do in a DNA interface that uses a single incarnation of the RotamerSets/InteractionGraph combo |
| DnaInterfacePackerCreator.hh | |
| DNAParameters.cc | A class to query for base-paired partners as well as base pair and base step parameters |
| DNAParameters.fwd.hh | |
| DNAParameters.hh | A class to query for base-paired partners as well as base pair and base step parameters |
| PDBOutput.cc | |
| PDBOutput.fwd.hh | |
| PDBOutput.hh | |
| RestrictDesignToProteinDNAInterface.cc | |
| RestrictDesignToProteinDNAInterface.fwd.hh | |
| RestrictDesignToProteinDNAInterface.hh | When operated on a PackerTask, pack/design is limited to the protein-DNA interface |
| RestrictDesignToProteinDNAInterfaceCreator.hh | |
| RotamerDNAHBondFilter.cc | Filters rotamers for contact to DNA in an -ex dependent manner |
| RotamerDNAHBondFilter.fwd.hh | |
| RotamerDNAHBondFilter.hh | Filters rotamers for contact to DNA in an -ex dependent manner |
| SeparateDnaFromNonDna.cc | |
| SeparateDnaFromNonDna.fwd.hh | |
| SeparateDnaFromNonDna.hh | |
| SeparateDnaFromNonDnaCreator.hh | |
| typedefs.hh | |
| util.cc | |
| util.hh | |
| WatsonCrickRotamerCouplings.cc | |
| WatsonCrickRotamerCouplings.fwd.hh | |
| WatsonCrickRotamerCouplings.hh | When operated on a PackerTask, adds RotamerCouplings to it that will trigger the use of a FixbbCoupledRotamerAnnealer by pack_rotamers, which will make base-paired DNA rotamer substitutions |
| WatsonCrickRotamerCouplingsCreator.hh | |
| ► docking | |
| ► stateless | |
| SaneDockingProtocol.cc | |
| SaneDockingProtocol.fwd.hh | |
| SaneDockingProtocol.hh | DockingProtocol class that doesn't use the more esoteric features of the Mover base class (e.g get_input_pose()) |
| ConformerSwitchMover.cc | Code for the conformer switch mover in ensemble docking |
| ConformerSwitchMover.fwd.hh | ConformerSwitchMover forward declarations header |
| ConformerSwitchMover.hh | |
| ConformerSwitchMoverCreator.hh | |
| DockFilters.cc | |
| DockFilters.fwd.hh | |
| DockFilters.hh | |
| DockingEnsemble.cc | Container class for ensemble docking information to be used with ConformerSwitchMover |
| DockingEnsemble.fwd.hh | |
| DockingEnsemble.hh | |
| DockingEnsemblePrepackProtocol.cc | Prepacking of the bound structure before docking with ensembles |
| DockingEnsemblePrepackProtocol.fwd.hh | |
| DockingEnsemblePrepackProtocol.hh | |
| DockingHighRes.cc | |
| DockingHighRes.fwd.hh | |
| DockingHighRes.hh | |
| DockingHighResLegacy.cc | |
| DockingHighResLegacy.fwd.hh | Forward declarations for DockingHighResLegacy (high resolution docking protocol as it existed in mini before the GrayLab refactor) |
| DockingHighResLegacy.hh | |
| DockingInitialPerturbation.cc | Initial position functions |
| DockingInitialPerturbation.fwd.hh | |
| DockingInitialPerturbation.hh | |
| DockingInitialPerturbationCreator.hh | |
| DockingLowRes.cc | |
| DockingLowRes.fwd.hh | |
| DockingLowRes.hh | |
| DockingLowResEnsemble.cc | |
| DockingLowResEnsemble.fwd.hh | |
| DockingLowResEnsemble.hh | |
| DockingPrepackProtocol.cc | Prepacking of the bound sturcture before docking |
| DockingPrepackProtocol.fwd.hh | |
| DockingPrepackProtocol.hh | |
| DockingProtocol.cc | |
| DockingProtocol.fwd.hh | |
| DockingProtocol.hh | |
| DockingProtocolCreator.hh | |
| DockMCMCycle.cc | |
| DockMCMCycle.fwd.hh | Forward declarations for DockMCMCycle (high resolution min) docking |
| DockMCMCycle.hh | |
| DockMCMProtocol.cc | |
| DockMCMProtocol.fwd.hh | Forward declarations for DockMCMProtocol (high resolution min) docking |
| DockMCMProtocol.hh | |
| DockMinMover.cc | |
| DockMinMover.fwd.hh | Forward declarations for DockMinMover (high resolution min) docking |
| DockMinMover.hh | |
| DockSetupMover.cc | |
| DockSetupMover.fwd.hh | |
| DockSetupMover.hh | Allows low-resolution docking using simulated or parallel tempering |
| DockSetupMoverCreator.hh | |
| DockTaskFactory.cc | |
| DockTaskFactory.fwd.hh | Forward declarations for DockTaskFactory |
| DockTaskFactory.hh | |
| EllipsoidalRandomizationMover.cc | |
| EllipsoidalRandomizationMover.fwd.hh | Forward declarations for EllipsoidalRandomizationMover (docking initial placement mover) |
| EllipsoidalRandomizationMover.hh | |
| metrics.cc | |
| metrics.hh | |
| RigidBodyInfo.cc | |
| RigidBodyInfo.fwd.hh | |
| RigidBodyInfo.hh | |
| SidechainMinMover.cc | |
| SidechainMinMover.fwd.hh | |
| SidechainMinMover.hh | |
| TemperedDocking.cc | |
| TemperedDocking.fwd.hh | |
| TemperedDocking.hh | Allows low-resolution docking using simulated or parallel tempering |
| TemperedDockingCreator.hh | |
| types.hh | Additionl types for Docking protocol |
| util.cc | |
| util.hh | |
| ► domain_assembly | |
| AddAssemblyConstraints.cc | -*- mode:c++;tab-width:2;indent-tabs-mode:t;show-trailing-whitespace:t;rm-trailing-spaces:t -*- |
| AddAssemblyConstraints.fwd.hh | -*- mode:c++;tab-width:2;indent-tabs-mode:t;show-trailing-whitespace:t;rm-trailing-spaces:t -*- |
| AddAssemblyConstraints.hh | |
| AssembleLinkerMover.cc | -*- mode:c++;tab-width:2;indent-tabs-mode:t;show-trailing-whitespace:t;rm-trailing-spaces:t -*- |
| AssembleLinkerMover.fwd.hh | -*- mode:c++;tab-width:2;indent-tabs-mode:t;show-trailing-whitespace:t;rm-trailing-spaces:t -*- |
| AssembleLinkerMover.hh | |
| CombineChainsMover.cc | -*- mode:c++;tab-width:2;indent-tabs-mode:t;show-trailing-whitespace:t;rm-trailing-spaces:t -*- |
| CombineChainsMover.fwd.hh | -*- mode:c++;tab-width:2;indent-tabs-mode:t;show-trailing-whitespace:t;rm-trailing-spaces:t -*- |
| CombineChainsMover.hh | |
| PostDockAssemblyScorer.cc | -*- mode:c++;tab-width:2;indent-tabs-mode:t;show-trailing-whitespace:t;rm-trailing-spaces:t -*- |
| PostDockAssemblyScorer.fwd.hh | -*- mode:c++;tab-width:2;indent-tabs-mode:t;show-trailing-whitespace:t;rm-trailing-spaces:t -*- |
| PostDockAssemblyScorer.hh | |
| ► electron_density | |
| BfactorFittingMover.cc | Set up morphing with electron density map |
| BfactorFittingMover.hh | |
| BfactorFittingMoverCreator.hh | |
| DensityMorphingMover.cc | Set up morphing with electron density map |
| DensityMorphingMover.hh | Add constraints to the current pose conformation |
| DensityMorphingMoverCreator.hh | |
| ReportFSC.cc | |
| ReportFSC.hh | |
| ReportFSCCreator.hh | |
| ScaleMapIntensities.cc | |
| ScaleMapIntensities.hh | |
| ScaleMapIntensitiesCreator.hh | |
| SetupForDensityScoringMover.cc | Protocols for folding into density |
| SetupForDensityScoringMover.hh | Protocols for folding into density |
| SetupForDensityScoringMoverCreator.hh | |
| util.cc | Protocols for folding into density |
| util.hh | Protocols for folding into density |
| ► elscripts | |
| ► modules | |
| MonteCarlo.hh | MonteCarlo module for ElScripts |
| BaseRole.cc | BaseRole, which handles a lot of common functions between all the elscripts roles including a lot of lua stuff |
| BaseRole.fwd.hh | Foward decls for BaseRole, base class of ElScripts |
| BaseRole.hh | BaseRole, which handles a lot of common functions between all the elscripts roles including a lot of lua stuff |
| Master.cc | The Master role in elscripts, handles trajectories, generating workunits, processing of results |
| Master.fwd.hh | Foward decls for Master, the master role of elscripts |
| Master.hh | The Master role in elscripts, handles trajectories, generating workunits, processing of results This is the non MPI version of the master, which is used by the Single Node Role Splitting this from MPI_Master so Single Node can be compiled without MPI |
| MPI_Master.cc | The MPI_Master role in elscripts, handles trajectories, generating workunits, processing of results |
| MPI_Master.fwd.hh | Foward decls for MPI_Master, the master role of elscripts |
| MPI_Master.hh | The MPI_Master role in elscripts, handles trajectories, generating workunits, processing of results Has additional functions related to boost mpi world and MPI_EndPoint |
| MPI_Slave.cc | Slave role of elscripts |
| MPI_Slave.fwd.hh | Foward decls for MPI_Slave, the slave role of elscripts |
| MPI_Slave.hh | Slave role of elscripts |
| SingleNode.cc | Slave role of elscripts |
| SingleNode.fwd.hh | Foward decls for SingleNode, the non mpi version of elscripts |
| SingleNode.hh | Singlenode role of elscripts |
| Slave.cc | Slave role of elscripts |
| Slave.fwd.hh | Foward decls for Slave, the slave role of elscripts |
| Slave.hh | Non_mpi slave role of elscripts used by single node, shares fxns with MPI_Slave |
| util.cc | |
| util.hh | Utility functions useful in elscripts |
| ► environment | |
| ► claims | |
| BrokerElements.cc | Some implementation details of the BrokerElements (such as they are) |
| BrokerElements.hh | |
| ClaimStrength.cc | ClaimStrength tracks the prioirty of a particular claim with respect to its initialization |
| ClaimStrength.fwd.hh | |
| ClaimStrength.hh | Header file for ClaimStrength, which tracks the prioirty of a particular claim with respect to its initialization |
| CutBiasClaim.cc | |
| CutBiasClaim.fwd.hh | |
| CutBiasClaim.hh | |
| EnvClaim.cc | |
| EnvClaim.fwd.hh | |
| EnvClaim.hh | |
| JumpClaim.cc | |
| JumpClaim.fwd.hh | |
| JumpClaim.hh | |
| TorsionClaim.cc | |
| TorsionClaim.fwd.hh | |
| TorsionClaim.hh | |
| VirtResClaim.cc | |
| VirtResClaim.fwd.hh | |
| VirtResClaim.hh | A claim for expressing the desire for new sequence to be inserted at a particular point |
| AutoCutData.cc | |
| AutoCutData.fwd.hh | Definition of the AutoCutData class |
| AutoCutData.hh | |
| AutoCutDataCreator.hh | |
| ClaimingMover.cc | |
| ClaimingMover.fwd.hh | Definition of the ClaimingMover class |
| ClaimingMover.hh | An environment that automatically distributes rights to shared degrees of freedom (e.g. fold tree) |
| DofUnlock.cc | |
| DofUnlock.fwd.hh | Definition of the DofUnlock class |
| DofUnlock.hh | A class that is used to express a mover-specific DoF-unlock on a ProtectedPose. Its destruction expresses a re-locking |
| EnvBeginMover.cc | |
| EnvBeginMover.fwd.hh | Definition of the EnvBeginMover class |
| EnvBeginMover.hh | |
| EnvClaimBroker.cc | |
| EnvClaimBroker.fwd.hh | Definition of the EnvClaimBroker class |
| EnvClaimBroker.hh | A class responsible for managing claims from ClaimingMovers, and retaining important information about the result of the brokering process |
| EnvEndMover.cc | |
| EnvEndMover.fwd.hh | Definition of the EnvEndMover class |
| EnvEndMover.hh | |
| EnvExcn.hh | A class that is used to express a mover-specific DoF-unlock on a ProtectedPose. Its destruction expresses a re-locking |
| Environment.cc | |
| Environment.fwd.hh | Definition of the BrokeredEnvironment class |
| Environment.hh | |
| ProtectedConformation.cc | |
| ProtectedConformation.fwd.hh | Definition of the ProtectedConformation class |
| ProtectedConformation.hh | A conformation built by the environment to be protected |
| ► enzdes | |
| AddLigandMotifRotamersOperationCreator.hh | |
| AddorRemoveCsts.cc | |
| AddorRemoveCsts.hh | |
| AddOrRemoveMatchCstsCreator.hh | |
| AddRigidBodyLigandConfsCreator.hh | |
| BackboneSampler.cc | |
| BackboneSampler.hh | Adapted from backrub mover in protein interface design |
| BackboneSamplerCreator.hh | |
| DesignVsNativeComparison.cc | |
| DesignVsNativeComparison.hh | |
| DetectProteinLigandInterfaceOperationCreator.hh | |
| enzdes_util.cc | Bunch of utility functions used in enzdes |
| enzdes_util.hh | Bunch of utility functions used in enzdes |
| EnzdesBaseProtocol.cc | |
| EnzdesBaseProtocol.fwd.hh | |
| EnzdesBaseProtocol.hh | |
| EnzdesFixBBProtocol.cc | |
| EnzdesFixBBProtocol.hh | |
| EnzdesFlexBBProtocol.cc | |
| EnzdesFlexBBProtocol.hh | |
| EnzdesJobInputter.cc | Job inputter that adds some stuff for enzdes to the pose |
| EnzdesJobInputter.fwd.hh | |
| EnzdesJobInputter.hh | |
| EnzdesJobInputterCreator.hh | |
| EnzdesJobOutputter.cc | Implementation for EnzdesJobOutputter |
| EnzdesJobOutputter.fwd.hh | Forward declaration for EnzdesJobOutputters |
| EnzdesJobOutputter.hh | |
| EnzdesJobOutputterCreator.hh | |
| EnzdesMovers.cc | |
| EnzdesMovers.fwd.hh | |
| EnzdesMovers.hh | Collection of movers that are used at different stages in enzyme design |
| EnzdesMoversCreator.hh | |
| EnzdesTaskOperations.cc | |
| EnzdesTaskOperations.fwd.hh | |
| EnzdesTaskOperations.hh | |
| EnzFilterCreators.hh | FilterCreators for the enzyme design filters |
| EnzFilters.cc | |
| EnzFilters.fwd.hh | |
| EnzFilters.hh | Definition of filter classes for enzdes in rosetta_scripts framework |
| EnzRepackMinimize.cc | Repack/minimize class for rosetta_scripts-compatible enzdes |
| EnzRepackMinimize.fwd.hh | |
| EnzRepackMinimize.hh | |
| EnzRepackMinimizeCreator.hh | |
| ModifyStoredLigandRBConfsMovers.cc | |
| ModifyStoredLigandRBConfsMovers.fwd.hh | |
| ModifyStoredLigandRBConfsMovers.hh | |
| PackRotamersMoverPartGreedy.cc | Partly greedy pack rotamers mover. given a set of target residues, choose their neighbors greedily and then |
| PackRotamersMoverPartGreedy.hh | |
| PackRotamersMoverPartGreedyCreator.hh | |
| ProteinLigandInterfaceUpweighterOperationCreator.hh | |
| RemoveLigandFilter.cc | |
| RemoveLigandFilter.fwd.hh | |
| RemoveLigandFilter.hh | |
| RemoveLigandFilterCreator.hh | |
| SecondaryMatchProtocol.cc | |
| SecondaryMatchProtocol.hh | |
| SetCatalyticResPackBehaviorCreator.hh | |
| ► evaluation | |
| AlignEvaluator.cc | |
| AlignEvaluator.fwd.hh | Forward declaration for AlignEvaluator class |
| AlignEvaluator.hh | |
| EvaluatorCreator.fwd.hh | Forward Header for base class for EvaluatorCreators for the Evaluator load-time factory registration scheme |
| EvaluatorCreator.hh | |
| EvaluatorFactory.cc | Factory for creating Evaluators objects |
| EvaluatorFactory.fwd.hh | Report data to database |
| EvaluatorFactory.hh | Factory for creating Evaluator objects |
| PCA.cc | |
| PCA.fwd.hh | |
| PCA.hh | |
| PoseEvaluator.cc | |
| PoseEvaluator.fwd.hh | |
| PoseEvaluator.hh | |
| TimeEvaluator.cc | |
| TimeEvaluator.fwd.hh | |
| TimeEvaluator.hh | |
| util.cc | |
| util.hh | |
| ► farna | |
| BasePairStep.cc | |
| BasePairStep.fwd.hh | |
| BasePairStep.hh | |
| BasePairStepLibrary.cc | |
| BasePairStepLibrary.fwd.hh | |
| BasePairStepLibrary.hh | |
| FullAtomRNA_Fragments.cc | |
| FullAtomRNA_Fragments.fwd.hh | |
| FullAtomRNA_Fragments.hh | |
| MultipleDomainMover.cc | |
| MultipleDomainMover.fwd.hh | Forward declarations header |
| MultipleDomainMover.hh | |
| RNA_BasePairClassifier.cc | |
| RNA_BasePairClassifier.hh | |
| RNA_ChunkLibrary.cc | |
| RNA_ChunkLibrary.fwd.hh | |
| RNA_ChunkLibrary.hh | Forward declarations header |
| RNA_DataReader.cc | |
| RNA_DataReader.fwd.hh | |
| RNA_DataReader.hh | |
| RNA_DeNovoProtocol.cc | |
| RNA_DeNovoProtocol.hh | |
| RNA_FragmentMover.cc | |
| RNA_FragmentMover.fwd.hh | |
| RNA_FragmentMover.hh | |
| RNA_Fragments.cc | |
| RNA_Fragments.fwd.hh | |
| RNA_Fragments.hh | |
| rna_fragments_classes.fwd.hh | |
| RNA_FragmentsClasses.cc | |
| RNA_FragmentsClasses.fwd.hh | |
| RNA_FragmentsClasses.hh | |
| RNA_JumpLibrary.cc | |
| RNA_JumpLibrary.fwd.hh | |
| RNA_JumpLibrary.hh | |
| RNA_LoopCloser.cc | |
| RNA_LoopCloser.fwd.hh | |
| RNA_LoopCloser.hh | |
| RNA_MatchType.hh | |
| RNA_Minimizer.cc | |
| RNA_Minimizer.fwd.hh | |
| RNA_Minimizer.hh | |
| RNA_ProtocolUtil.cc | |
| RNA_ProtocolUtil.hh | |
| RNA_Relaxer.cc | |
| RNA_Relaxer.fwd.hh | |
| RNA_Relaxer.hh | |
| RNA_SecStructInfo.cc | |
| RNA_SecStructInfo.fwd.hh | |
| RNA_SecStructInfo.hh | |
| RNA_StructureParameters.cc | |
| RNA_StructureParameters.fwd.hh | |
| RNA_StructureParameters.hh | |
| ► features | |
| ► helixAssembly | |
| ConcurrencyTest.cc | |
| ConcurrencyTest.fwd.hh | |
| ConcurrencyTest.hh | |
| ConcurrencyTestCreator.cc | |
| ConcurrencyTestCreator.hh | |
| HelicalFragment.cc | |
| HelicalFragment.fwd.hh | |
| HelicalFragment.hh | Small helper class that stores the start and end of a helix secondary structure |
| HelixBundleFeatures.cc | Search through a pose for sets of 3 helices and generate RMSD calculations between all pairs of them |
| HelixBundleFeatures.fwd.hh | |
| HelixBundleFeatures.hh | |
| HelixBundleFeaturesCreator.cc | |
| HelixBundleFeaturesCreator.hh | |
| ► strand_assembly | |
| SandwichFeatures.cc | Extract and analyze beta-sandwich features |
| SandwichFeatures.fwd.hh | |
| SandwichFeatures.hh | |
| SandwichFeaturesCreator.cc | |
| SandwichFeaturesCreator.hh | |
| SandwichFragment.cc | |
| SandwichFragment.hh | Small helper class that stores the start and end of a strand secondary structure |
| StrandBundleFeatures.cc | Extract beta strand, strand pairs, sandwiches in pdb file, see wiki.rosettacommons.org/index.php/MultiBodyFeaturesReporters#StrandBundleFeatures for detail |
| StrandBundleFeatures.fwd.hh | |
| StrandBundleFeatures.hh | Extract beta strand, strand pairs, sandwiches in pdb file, see wiki.rosettacommons.org/index.php/MultiBodyFeaturesReporters#StrandBundleFeatures for detail |
| StrandBundleFeaturesCreator.cc | |
| StrandBundleFeaturesCreator.hh | |
| StrandFragment.cc | |
| StrandFragment.hh | Small helper class that stores the start and end of a strand secondary structure |
| AtomAtomPairFeatures.cc | Report atom-atom pair geometry and scores to features statistics scientific benchmark |
| AtomAtomPairFeatures.fwd.hh | Report atom-atom pair geometry and scores to features Statistics Scientific Benchmark |
| AtomAtomPairFeatures.hh | Report atom-atom pair geometry and scores to features Statistics Scientific Benchmark |
| AtomAtomPairFeaturesCreator.cc | |
| AtomAtomPairFeaturesCreator.hh | Header for AtomAtomPairFeaturesCreator for the AtomAtomPairFeatures load-time factory registration scheme |
| AtomInResidueAtomInResiduePairFeatures.cc | Report atom-atom pair geometry and scores to features statistics scientific benchmark |
| AtomInResidueAtomInResiduePairFeatures.fwd.hh | Report atom-atom pair geometry and scores to features Statistics Scientific Benchmark |
| AtomInResidueAtomInResiduePairFeatures.hh | Report atom-atom pair geometry and scores to features Statistics Scientific Benchmark |
| AtomInResidueAtomInResiduePairFeaturesCreator.cc | |
| AtomInResidueAtomInResiduePairFeaturesCreator.hh | Header for AtomInResidueAtomInResiduePairFeaturesCreator for the AtomInResidueAtomInResiduePairFeatures load-time factory registration scheme |
| AtomTypesFeatures.cc | Report AtomType properties to features Statistics Scientific Benchmark |
| AtomTypesFeatures.fwd.hh | Report AtomTypes geometry and scores to features Statistics Scientific Benchmark |
| AtomTypesFeatures.hh | Report AtomType features Statistics Scientific Benchmark |
| AtomTypesFeaturesCreator.cc | |
| AtomTypesFeaturesCreator.hh | Header for AtomTypesFeaturesCreator for the AtomTypesFeatures load-time factory registration scheme |
| BatchFeatures.cc | |
| BatchFeatures.fwd.hh | |
| BatchFeatures.hh | |
| BatchFeaturesCreator.cc | |
| BatchFeaturesCreator.hh | |
| BetaTurnDetectionFeatures.cc | Report comments stored with each pose |
| BetaTurnDetectionFeatures.fwd.hh | Report residue level geometry and scores to features Statistics Scientific Benchmark |
| BetaTurnDetectionFeatures.hh | |
| BetaTurnDetectionFeaturesCreator.cc | |
| BetaTurnDetectionFeaturesCreator.hh | Header for BetaTurnDetectionFeaturesCreator for the BetaTurnDetectionFeatures load-time factory registration scheme |
| ChargeChargeFeatures.cc | Report geometric solvation energy for each polar site to a features database |
| ChargeChargeFeatures.fwd.hh | Report geometric solvation for each polar site to features Statistics Scientific Benchmark |
| ChargeChargeFeatures.hh | Report comments stored with each pose |
| ChargeChargeFeaturesCreator.cc | |
| ChargeChargeFeaturesCreator.hh | Header for ChargeChargeFeaturesCreator for the ChargeChargeFeatures load-time factory registration scheme |
| DatabaseFilters.cc | |
| DatabaseFilters.fwd.hh | Report data to database |
| DatabaseFilters.hh | Report atom-atom pair geometry and scores to features Statistics Scientific Benchmark |
| DatabaseJobInputter.cc | |
| DatabaseJobInputter.fwd.hh | |
| DatabaseJobInputter.hh | Header file for DatabaseJobInputter class |
| DatabaseJobInputterCreator.hh | |
| DatabaseJobOutputter.cc | Job Outputter to a database |
| DatabaseJobOutputter.fwd.hh | Header file for DatabaseJobOutputter class |
| DatabaseJobOutputter.hh | Header file for DatabaseJobOutputter class |
| DatabaseJobOutputterCreator.hh | |
| DatabaseStatements.cc | |
| DatabaseStatements.hh | |
| FeaturesReporter.cc | Base class to report geometry and scores to features Statistics Scientific Benchmark |
| FeaturesReporter.fwd.hh | Report data to database |
| FeaturesReporter.hh | Base class to report geometry and scores to features Statistics Scientific Benchmark |
| FeaturesReporterCreator.fwd.hh | |
| FeaturesReporterCreator.hh | |
| FeaturesReporterFactory.cc | Factory for creating FeaturesReporters objects |
| FeaturesReporterFactory.fwd.hh | Report data to database |
| FeaturesReporterFactory.hh | Factory for creating FeaturesReporter objects |
| GeometricSolvationFeatures.cc | Report geometric solvation energy for each polar site to a features database |
| GeometricSolvationFeatures.fwd.hh | Report geometric solvation for each polar site to features Statistics Scientific Benchmark |
| GeometricSolvationFeatures.hh | Report hydrogen bonding based solvation model to a features database |
| GeometricSolvationFeaturesCreator.cc | |
| GeometricSolvationFeaturesCreator.hh | Header for GeometricSolvationFeaturesCreator for the GeometricSolvationFeatures load-time factory registration scheme |
| HBondFeatures.cc | Report HBond geometry and scores to features Statistics Scientific Benchmark |
| HBondFeatures.fwd.hh | Report HBond geometry and scores to features Statistics Scientific Benchmark |
| HBondFeatures.hh | Report HBond geometry and scores to features Statistics Scientific Benchmark |
| HBondFeaturesCreator.cc | |
| HBondFeaturesCreator.hh | Header for HBondFeaturesCreator for the HBondFeatures load-time factory registration scheme |
| HBondParameterFeatures.cc | Report HBond Parameters to features Statistics Scientific Benchmark |
| HBondParameterFeatures.fwd.hh | Report HBondParameter geometry and scores to features Statistics Scientific Benchmark |
| HBondParameterFeatures.hh | Report HBond Parameter features Statistics Scientific Benchmark |
| HBondParameterFeaturesCreator.cc | |
| HBondParameterFeaturesCreator.hh | Header for HBondParameterFeaturesCreator for the HBondParameterFeatures load-time factory registration scheme |
| InterfaceFeatures.cc | |
| InterfaceFeatures.fwd.hh | |
| InterfaceFeatures.hh | Analyzes interfaces and interface residues of a pose mainly using InterfaceAnalayzerMover |
| InterfaceFeaturesCreator.cc | |
| InterfaceFeaturesCreator.hh | |
| JobDataFeatures.cc | |
| JobDataFeatures.fwd.hh | |
| JobDataFeatures.hh | |
| JobDataFeaturesCreator.cc | |
| JobDataFeaturesCreator.hh | Header for JobDataFeaturesCreator for the JobDataFeatures load-time factory registration scheme |
| LoopAnchorFeatures.cc | Report loop anchor features to a features database |
| LoopAnchorFeatures.fwd.hh | Report residue level geometry and scores to features Statistics Scientific Benchmark |
| LoopAnchorFeatures.hh | Report comments stored with each pose |
| LoopAnchorFeaturesCreator.cc | |
| LoopAnchorFeaturesCreator.hh | Header for LoopAnchorFeaturesCreator for the LoopAnchorFeatures load-time factory registration scheme |
| OrbitalsFeatures.cc | Report orbital geometry and scores to features statistics scientific benchmark |
| OrbitalsFeatures.fwd.hh | Report Orbital geometry and scores to features Statistics Scientific Benchmark |
| OrbitalsFeatures.hh | Report Orbital geometry and scores to features Statistics Scientific Benchmark |
| OrbitalsFeaturesCreator.cc | |
| OrbitalsFeaturesCreator.hh | Header for OrbitalsFeaturesCreator for the OrbitalsFeatures load-time factory registration scheme |
| PairFeatures.cc | Report orbital geometry and scores to features statistics scientific benchmark |
| PairFeatures.fwd.hh | Report atom-atom pair geometry and scores to features Statistics Scientific Benchmark |
| PairFeatures.hh | Report residue and atom pair geometry and scores to features Statistics Scientific Benchmark |
| PairFeaturesCreator.cc | |
| PairFeaturesCreator.hh | Header for PairFeaturesCreator for the PairFeatures load-time factory registration scheme |
| PdbDataFeatures.cc | |
| PdbDataFeatures.fwd.hh | |
| PdbDataFeatures.hh | |
| PdbDataFeaturesCreator.cc | |
| PdbDataFeaturesCreator.hh | Header for PdbDataFeaturesCreator for the PdbDataFeatures load-time factory registration scheme |
| PoseCommentsFeatures.cc | Report comments stored with each pose |
| PoseCommentsFeatures.fwd.hh | Report residue level geometry and scores to features Statistics Scientific Benchmark |
| PoseCommentsFeatures.hh | Report comments stored with each pose |
| PoseCommentsFeaturesCreator.cc | |
| PoseCommentsFeaturesCreator.hh | Header for PoseCommentsFeaturesCreator for the PoseCommentsFeatures load-time factory registration scheme |
| PoseConformationFeatures.cc | Report comments stored with each pose |
| PoseConformationFeatures.fwd.hh | Report pose fold tree related features |
| PoseConformationFeatures.hh | Report comments stored with each pose |
| PoseConformationFeaturesCreator.cc | |
| PoseConformationFeaturesCreator.hh | Header for PoseConformationFeaturesCreator for the PoseConformationFeatures load-time factory registration scheme |
| ProteinBackboneAtomAtomPairFeatures.cc | Report atom-atom pair distances between atoms in protein backbones to features Statistics Scientific Benchmark |
| ProteinBackboneAtomAtomPairFeatures.fwd.hh | Report atom-atom pair distances between atoms in protein backbones to features Statistics Scientific Benchmark |
| ProteinBackboneAtomAtomPairFeatures.hh | Report atom-atom pair distances between atoms in protein backbones to features Statistics Scientific Benchmark |
| ProteinBackboneAtomAtomPairFeaturesCreator.cc | |
| ProteinBackboneAtomAtomPairFeaturesCreator.hh | Header for ProteinBackboneAtomAtomPairFeaturesCreator for the ProteinBackboneAtomAtomPairFeatures load-time factory registration scheme |
| ProteinBackboneTorsionAngleFeatures.cc | Report Backbone Torsional Angle features |
| ProteinBackboneTorsionAngleFeatures.fwd.hh | Report protein backbone torsion angle features |
| ProteinBackboneTorsionAngleFeatures.hh | Report protein backbone torsion angle features |
| ProteinBackboneTorsionAngleFeaturesCreator.cc | |
| ProteinBackboneTorsionAngleFeaturesCreator.hh | Header for ProteinBackboneTorsionAngleFeaturesCreator for the ProteinBackboneTorsionAngleFeatures load-time factory registration scheme |
| ProteinBondGeometryFeatures.cc | Report Backbone Torsional Angle features |
| ProteinBondGeometryFeatures.fwd.hh | Report protein bond geometry features |
| ProteinBondGeometryFeatures.hh | Report protein backbone torsion angle features |
| ProteinBondGeometryFeaturesCreator.cc | |
| ProteinBondGeometryFeaturesCreator.hh | Header for ProteinBondGeometryFeaturesCreator for the ProteinBondGeometryFeatures load-time factory registration scheme |
| ProteinResidueConformationFeatures.cc | Report idealized torsional DOFs Statistics Scientific Benchmark |
| ProteinResidueConformationFeatures.fwd.hh | Report residue level geometry and scores to features Statistics Scientific Benchmark |
| ProteinResidueConformationFeatures.hh | Report idealized torsional DOFs Statistics Scientific Benchmark |
| ProteinResidueConformationFeaturesCreator.cc | |
| ProteinResidueConformationFeaturesCreator.hh | Header for ProteinResidueConformationFeaturesCreator for the ProteinResidueConformationFeatures load-time factory registration scheme |
| ProteinRMSDFeatures.cc | Report the root mean squared deviation between two poses |
| ProteinRMSDFeatures.fwd.hh | Report RMSD similarity of a protein structure against supplied reference structure |
| ProteinRMSDFeatures.hh | Report ProteinRMSD similarity of structure against supplied reference structure |
| ProteinRMSDFeaturesCreator.cc | |
| ProteinRMSDFeaturesCreator.hh | Header for ProteinRMSDFeaturesCreator for the ProteinRMSDFeatures load-time factory registration scheme |
| ProteinRMSDNoSuperpositionFeatures.cc | Report the root mean squared deviation (without superposition) between two poses |
| ProteinRMSDNoSuperpositionFeatures.fwd.hh | Report (no superposition) RMSD similarity of a protein structure against supplied reference structure |
| ProteinRMSDNoSuperpositionFeatures.hh | Report ProteinRMSD similarity of structure against supplied reference structure without superposition |
| ProteinRMSDNoSuperpositionFeaturesCreator.cc | |
| ProteinRMSDNoSuperpositionFeaturesCreator.hh | Header for ProteinRMSDNoSuperpositionFeaturesCreator for the ProteinRMSDNoSuperpositionFeatures load-time factory registration scheme |
| ProteinSilentReport.cc | |
| ProteinSilentReport.fwd.hh | Report pose fold tree related features |
| ProteinSilentReport.hh | Report feature data to database |
| ProtocolFeatures.cc | Report protocol level features to features statistics scientific benchmark |
| ProtocolFeatures.fwd.hh | Report Orbital geometry and scores to features Statistics Scientific Benchmark |
| ProtocolFeatures.hh | Report Orbital geometry and scores to features Statistics Scientific Benchmark |
| ProtocolFeaturesCreator.cc | |
| ProtocolFeaturesCreator.hh | Header for ProtocolFeaturesCreator for the ProtocolFeatures load-time factory registration scheme |
| RadiusOfGyrationFeatures.cc | Report the radius of gyration to features Statistics Scientific Benchmark |
| RadiusOfGyrationFeatures.fwd.hh | Report the radius of gyration to features Statistics Scientific Benchmark |
| RadiusOfGyrationFeatures.hh | Report the radius of gyration to features Statistics Scientific Benchmark |
| RadiusOfGyrationFeaturesCreator.cc | |
| RadiusOfGyrationFeaturesCreator.hh | Header for RadiusOfGyrationFeaturesCreator for the RadiusOfGyrationFeatures load-time factory registration scheme |
| Report.cc | |
| Report.fwd.hh | Report pose fold tree related features |
| Report.hh | Report feature data to database |
| ReportToDB.cc | Report all data to a database |
| ReportToDB.fwd.hh | Report data to sqlite database |
| ReportToDB.hh | Report feature data to sqlite database |
| ReportToDBCreator.hh | This class will create instances of Mover ReportToDB for the MoverFactory |
| ResidueBurialFeatures.cc | Report residue burial to features statistics scientific benchmark |
| ResidueBurialFeatures.fwd.hh | Report residue level geometry and scores to features Statistics Scientific Benchmark |
| ResidueBurialFeatures.hh | Report residue to features Statistics Scientific Benchmark |
| ResidueBurialFeaturesCreator.cc | |
| ResidueBurialFeaturesCreator.hh | Header for ResidueBurialFeaturesCreator for the ResidueBurialFeatures load-time factory registration scheme |
| ResidueConformationFeatures.cc | Report idealized torsional DOFs Statistics Scientific Benchmark |
| ResidueConformationFeatures.fwd.hh | Report residue level geometry and scores to features Statistics Scientific Benchmark |
| ResidueConformationFeatures.hh | |
| ResidueConformationFeaturesCreator.cc | |
| ResidueConformationFeaturesCreator.hh | Header for ResidueConformationFeaturesCreator for the ResidueConformationFeatures load-time factory registration scheme |
| ResidueFeatures.cc | Report residue features to features Statistics Scientific Benchmark |
| ResidueFeatures.fwd.hh | Report residue features to features Statistics Scientific Benchmark |
| ResidueFeatures.hh | Report residue to features Statistics Scientific Benchmark |
| ResidueFeaturesCreator.cc | |
| ResidueFeaturesCreator.hh | Header for ResidueFeaturesCreator for the ResidueFeatures load-time factory registration scheme |
| ResidueGridScoresFeatures.cc | Detailed per atom scores of Scoring Grids |
| ResidueGridScoresFeatures.fwd.hh | |
| ResidueGridScoresFeatures.hh | |
| ResidueGridScoresFeaturesCreator.hh | |
| ResidueScoresFeatures.cc | Report residue scores to features Statistics Scientific Benchmark |
| ResidueScoresFeatures.fwd.hh | Report residue scores to features Statistics Scientific Benchmark |
| ResidueScoresFeatures.hh | Report residue scores to features Statistics Scientific Benchmark |
| ResidueScoresFeaturesCreator.cc | |
| ResidueScoresFeaturesCreator.hh | Header for ResidueScoresFeaturesCreator for the ResidueScoresFeatures load-time factory registration scheme |
| ResidueSecondaryStructureFeatures.cc | Report ResidueSecondaryStructure geometry and scores to features Statistics Scientific Benchmark |
| ResidueSecondaryStructureFeatures.fwd.hh | Report ResidueSecondaryStructure geometry and scores to features Statistics Scientific Benchmark |
| ResidueSecondaryStructureFeatures.hh | Report ResidueSecondaryStructure geometry and scores to features Statistics Scientific Benchmark |
| ResidueSecondaryStructureFeaturesCreator.cc | |
| ResidueSecondaryStructureFeaturesCreator.hh | Header for ResidueSecondaryStructureFeaturesCreator for the ResidueSecondaryStructureFeatures load-time factory registration scheme |
| ResidueTotalScoresFeatures.cc | Report the total per residue score to a features database |
| ResidueTotalScoresFeatures.fwd.hh | Report the total per residue score to a features database |
| ResidueTotalScoresFeatures.hh | Report the total per residue score to a features database |
| ResidueTotalScoresFeaturesCreator.cc | |
| ResidueTotalScoresFeaturesCreator.hh | Header for ResidueTotalScoresFeaturesCreator for the ResidueTotalScoresFeatures load-time factory registration scheme |
| ResidueTypesFeatures.cc | Report ResidueTypes to features Statistics Scientific Benchmark |
| ResidueTypesFeatures.fwd.hh | Report ResidueTypes geometry and scores to features Statistics Scientific Benchmark |
| ResidueTypesFeatures.hh | Report ResidueTypes features Statistics Scientific Benchmark |
| ResidueTypesFeaturesCreator.cc | |
| ResidueTypesFeaturesCreator.hh | Header for ResidueTypesFeaturesCreator for the ResidueTypesFeatures load-time factory registration scheme |
| RotamerBoltzmannWeightFeatures.cc | Report residue burial to features statistics scientific benchmark |
| RotamerBoltzmannWeightFeatures.fwd.hh | Report rotamer boltzmann weights to features Statistics Scientific Benchmark |
| RotamerBoltzmannWeightFeatures.hh | Report rotamer boltzmann weights to features Statistics Scientific Benchmark |
| RotamerBoltzmannWeightFeaturesCreator.cc | |
| RotamerBoltzmannWeightFeaturesCreator.hh | Header for RotamerBoltzmannWeightFeaturesCreator for the RotamerBoltzmannWeightFeatures load-time factory registration scheme |
| RotamerFeatures.cc | Report rotamer library features to the database |
| RotamerFeatures.fwd.hh | Report residue level geometry and scores to features Statistics Scientific Benchmark |
| RotamerFeatures.hh | Report idealized torsional DOFs Statistics Scientific Benchmark |
| RotamerFeaturesCreator.cc | |
| RotamerFeaturesCreator.hh | Header for RotamerFeaturesCreator for the RotamerFeatures load-time factory registration scheme |
| RotamerRecoveryFeatures.cc | Report rotamer recover features and scores to features Statistics Scientific Benchmark |
| RotamerRecoveryFeatures.fwd.hh | Report Rotamer Recovery features to features Statistics Scientific Benchmark |
| RotamerRecoveryFeatures.hh | Report Rotamer Recovery Statistics Scientific Benchmark |
| RotamerRecoveryFeaturesCreator.cc | |
| RotamerRecoveryFeaturesCreator.hh | Header for RotamerRecoveryFeaturesCreator for the RotamerRecoveryFeatures load-time factory registration scheme |
| SaltBridgeFeatures.cc | Report geometric solvation energy for each polar site to a features database |
| SaltBridgeFeatures.fwd.hh | Report geometric solvation for each polar site to features Statistics Scientific Benchmark |
| SaltBridgeFeatures.hh | Report comments stored with each pose |
| SaltBridgeFeaturesCreator.cc | |
| SaltBridgeFeaturesCreator.hh | Header for SaltBridgeFeaturesCreator for the SaltBridgeFeatures load-time factory registration scheme |
| ScoreFunctionFeatures.cc | Report the score parameters to a features database |
| ScoreFunctionFeatures.fwd.hh | Structure scores to features Statistics Scientific Benchmark |
| ScoreFunctionFeatures.hh | Add score function parameters to a features database |
| ScoreFunctionFeaturesCreator.cc | |
| ScoreFunctionFeaturesCreator.hh | Header for ScoreFunctionFeaturesCreator for the ScoreFunctionFeatures load-time factory registration scheme |
| ScoreTypeFeatures.cc | Report protocol level features to features statistics scientific benchmark |
| ScoreTypeFeatures.fwd.hh | Structure scores to features Statistics Scientific Benchmark |
| ScoreTypeFeatures.hh | Structure scores to features Statistics Scientific Benchmark |
| ScoreTypeFeaturesCreator.cc | |
| ScoreTypeFeaturesCreator.hh | Header for ScoreTypeFeaturesCreator for the ScoreTypeFeatures load-time factory registration scheme |
| ScreeningFeatures.cc | Report JSON object with information needed for vHTS postprocessing |
| ScreeningFeatures.fwd.hh | Forward headers for ScreeningFeatuers |
| ScreeningFeatures.hh | Report JSON object with information needed for vHTS postprocessing |
| ScreeningFeaturesCreator.cc | |
| ScreeningFeaturesCreator.hh | |
| SecondaryStructureSegmentFeatures.cc | |
| SecondaryStructureSegmentFeatures.fwd.hh | |
| SecondaryStructureSegmentFeatures.hh | |
| SecondaryStructureSegmentFeaturesCreator.cc | |
| SecondaryStructureSegmentFeaturesCreator.hh | |
| SmotifFeatures.cc | Calculate 4 geometric values used to classify smotifs. Reference (http://www.ncbi.nlm.nih.gov/pubmed/20421995) |
| SmotifFeatures.fwd.hh | |
| SmotifFeatures.hh | |
| SmotifFeaturesCreator.cc | |
| SmotifFeaturesCreator.hh | |
| StructureFeatures.cc | |
| StructureFeatures.fwd.hh | Report structure features to features Statistics Scientific Benchmark |
| StructureFeatures.hh | Report structure identifiers to a features database |
| StructureFeaturesCreator.cc | |
| StructureFeaturesCreator.hh | Header for StructureFeaturesCreator for the StructureFeatures load-time factory registration scheme |
| StructureScoresFeatures.cc | Report structure score features to a features database |
| StructureScoresFeatures.fwd.hh | Structure scores to features Statistics Scientific Benchmark |
| StructureScoresFeatures.hh | Structure scores to features Statistics Scientific Benchmark |
| StructureScoresFeaturesCreator.cc | |
| StructureScoresFeaturesCreator.hh | Header for StructureScoresFeaturesCreator for the StructureScoresFeatures load-time factory registration scheme |
| UnrecognizedAtomFeatures.cc | Report unrecognized atoms features to features Statistics Scientific Benchmark |
| UnrecognizedAtomFeatures.fwd.hh | Report residue features to features Statistics Scientific Benchmark |
| UnrecognizedAtomFeatures.hh | Report residue to features Statistics Scientific Benchmark |
| UnrecognizedAtomFeaturesCreator.cc | |
| UnrecognizedAtomFeaturesCreator.hh | Header for UnrecognizedAtomFeaturesCreator for the UnrecognizedAtomFeatures load-time factory registration scheme |
| util.cc | |
| util.hh | |
| ► fibril | |
| fibril_util.cc | |
| fibril_util.hh | Utility functions for handling of fibril symmetry modeling |
| SetupForFibrilMover.cc | |
| SetupForFibrilMover.fwd.hh | |
| SetupForFibrilMover.hh | |
| ► filters | |
| BasicFilterCreators.hh | FilterCreators for the most basic of filters |
| BasicFilters.cc | |
| BasicFilters.fwd.hh | |
| BasicFilters.hh | Header file for very simple Filter classes |
| CalculatorFilter.cc | Combine several filters in a (semi) arbitrary calculation |
| CalculatorFilter.fwd.hh | |
| CalculatorFilter.hh | Combine several filters in a (semi) arbitrary calculation |
| CalculatorFilterCreator.hh | FilterCreator for the CalculatorFilter |
| ContingentFilter.cc | |
| ContingentFilter.fwd.hh | |
| ContingentFilter.hh | A filter that is contingent on some other mover to set its pass/fail value |
| ContingentFilterCreator.hh | FilterCreator for the ContingentFilter |
| Filter.cc | |
| Filter.fwd.hh | |
| Filter.hh | Header file for Filter base class |
| FilterCreator.cc | |
| FilterCreator.hh | Base class for FilterCreators for the Filter load-time factory registration scheme |
| FilterFactory.cc | |
| FilterFactory.fwd.hh | Forward declaration of Factory class for Filters |
| FilterFactory.hh | |
| HeavyAtomFilter.cc | |
| HeavyAtomFilter.hh | |
| ReplicateFilter.cc | Repeat a subfilter multiple times, and pass a value based on the aggregate results |
| ReplicateFilter.fwd.hh | |
| ReplicateFilter.hh | Repeat a subfilter multiple times, and pass a value based on the aggregate results |
| ReplicateFilterCreator.hh | FilterCreator for the ReplicateFilter |
| TimeFilter.cc | |
| TimeFilter.hh | |
| TimeFilterCreator.hh | FilterCreator for the TimeFilter |
| ► fldsgn | |
| ► filters | |
| CoreDunbrackFilter.cc | |
| CoreDunbrackFilter.fwd.hh | |
| CoreDunbrackFilter.hh | Header file for CoreDunbrackFilter class |
| CoreDunbrackFilterCreator.hh | FilterCreators for the CoreDunbrackFilter |
| FragQualFilter.cc | |
| FragQualFilter.fwd.hh | |
| FragQualFilter.hh | Header file for FragQualFilter class |
| FragQualFilterCreator.hh | FilterCreators for the FragQualFilter |
| HelixKinkFilter.cc | |
| HelixKinkFilter.fwd.hh | |
| HelixKinkFilter.hh | Header file for HelixKinkFilter class |
| HelixKinkFilterCreator.hh | FilterCreators for the HelixKinkFilter |
| HelixPairingFilter.cc | |
| HelixPairingFilter.fwd.hh | |
| HelixPairingFilter.hh | Header file for HelixPairingFilter class |
| HelixPairingFilterCreator.hh | FilterCreators for the HelixPairingFilter |
| HSSTripletFilter.cc | |
| HSSTripletFilter.fwd.hh | |
| HSSTripletFilter.hh | Header file for HSSTripletFilter class |
| HSSTripletFilterCreator.hh | FilterCreators for the HSSTripletFilter |
| InterlockingAromaFilter.cc | |
| InterlockingAromaFilter.fwd.hh | |
| InterlockingAromaFilter.hh | Header file for InterlockingAromaFilter class |
| InterlockingAromaFilterCreator.hh | FilterCreators for the InterlockingAromaFilter |
| NcontactsFilter.cc | |
| NcontactsFilter.fwd.hh | |
| NcontactsFilter.hh | Header file for NcontactsFilter class |
| NcontactsFilterCreator.hh | FilterCreators for the NcontactsFilter |
| ParallelBetaPairingPreferenceFilter.cc | |
| ParallelBetaPairingPreferenceFilter.fwd.hh | |
| ParallelBetaPairingPreferenceFilter.hh | Header file for ParallelBetaPairingPreferenceFilter class |
| ParallelBetaPairingPreferenceFilterCreator.hh | FilterCreators for the ParallelBetaPairingPreferenceFilter |
| SecondaryStructureCountFilter.cc | |
| SecondaryStructureCountFilter.fwd.hh | |
| SecondaryStructureCountFilter.hh | Header file for SecondaryStructureCountFilter class |
| SecondaryStructureCountFilterCreator.hh | FilterCreators for the SecondaryStructureCountFilter |
| SecondaryStructureFilter.cc | |
| SecondaryStructureFilter.fwd.hh | |
| SecondaryStructureFilter.hh | Header file for SecondaryStructureFilter class |
| SecondaryStructureFilterCreator.hh | FilterCreators for the SecondaryStructureFilter |
| SheetTopologyFilter.cc | |
| SheetTopologyFilter.fwd.hh | |
| SheetTopologyFilter.hh | Header file for SheetTopologyFilter class |
| SheetTopologyFilterCreator.hh | FilterCreators for the SheetTopologyFilter |
| ► potentials | |
| ► sspot | |
| HSPairPotential.cc | |
| HSPairPotential.fwd.hh | |
| HSPairPotential.hh | |
| NatbiasHelicesSheetPotential.cc | Native-biased centroid score for helices on sheets |
| NatbiasHelicesSheetPotential.fwd.hh | |
| NatbiasHelicesSheetPotential.hh | Centroid score for helices on sheet |
| NatbiasHelixPairPotential.cc | Calss for helix-pairing potential |
| NatbiasHelixPairPotential.fwd.hh | |
| NatbiasHelixPairPotential.hh | |
| NatbiasSecondaryStructureEnergy.cc | Native biased centroid score for secondary structures |
| NatbiasSecondaryStructureEnergy.fwd.hh | |
| NatbiasSecondaryStructureEnergy.hh | Native biased centroid score for secondary structure |
| NatbiasSecondaryStructureEnergyCreator.hh | Declaration for the class that connects NatbiasSecondaryStructureEnergy with the ScoringManager |
| NatbiasSheetPotential.cc | Header file of NatbiasSheetPotential |
| NatbiasSheetPotential.fwd.hh | |
| NatbiasSheetPotential.hh | |
| NatbiasStrandPairPotential.cc | |
| NatbiasStrandPairPotential.fwd.hh | |
| NatbiasStrandPairPotential.hh | Native biased centroid score for strand pairings |
| SSPairPotential.cc | |
| SSPairPotential.fwd.hh | |
| SSPairPotential.hh | |
| util.cc | |
| util.hh | Helper functions for SSPairPotential and HSPairPotential |
| AACompositionEnergy.cc | |
| AACompositionEnergy.fwd.hh | |
| AACompositionEnergy.hh | Amino acid composition energy |
| AACompositionEnergyCreator.hh | |
| SetAACompositionPotential.cc | |
| SetAACompositionPotential.fwd.hh | |
| SetAACompositionPotential.hh | |
| SetAACompositionPotentialCreator.hh | |
| SetSecStructEnergies.cc | |
| SetSecStructEnergies.fwd.hh | |
| SetSecStructEnergies.hh | Mover for setting centroid score of secondary structure through parser |
| SetSecStructEnergiesCreator.hh | |
| ► topology | |
| BB_Pos.cc | |
| BB_Pos.fwd.hh | |
| BB_Pos.hh | Bb_pos class header |
| BetaAlphaBetaMotif.cc | |
| BetaAlphaBetaMotif.fwd.hh | |
| BetaAlphaBetaMotif.hh | |
| DimerPairing.cc | |
| DimerPairing.fwd.hh | |
| DimerPairing.hh | |
| HelixPairing.cc | Class for helix pairings |
| HelixPairing.fwd.hh | |
| HelixPairing.hh | Header file of HelixPairing.cc |
| HSSTriplet.cc | |
| HSSTriplet.fwd.hh | |
| HSSTriplet.hh | |
| Sheet.cc | |
| Sheet.fwd.hh | |
| Sheet.hh | |
| SheetFoldTypeManager.cc | |
| SheetFoldTypeManager.fwd.hh | |
| SheetFoldTypeManager.hh | |
| SS_Info2.cc | |
| SS_Info2.fwd.hh | |
| SS_Info2.hh | |
| StrandPairing.cc | |
| StrandPairing.fwd.hh | |
| StrandPairing.hh | |
| util.cc | Utilities for fldsgn/topology |
| util.hh | |
| BluePrintBDR.cc | |
| BluePrintBDR.fwd.hh | Forward declaration for BluePrintBDR |
| BluePrintBDR.hh | |
| BluePrintBDRCreator.hh | This class will create instances of Mover BluePrintBDR for the MoverFactory |
| CircularPermutation.cc | Perform circularpermutation give a pose ( under development ) |
| CircularPermutation.fwd.hh | Forward declaration for CircularPermutation |
| CircularPermutation.hh | |
| CircularPermutationCreator.hh | |
| MatchResidues.cc | |
| MatchResidues.hh | Header file for MatchResidues class |
| MatchResiduesMover.cc | |
| MatchResiduesMover.fwd.hh | |
| MatchResiduesMover.hh | Header file for MatchResiduesMover class |
| MatchResiduesMoverCreator.hh | MoverCreator for the MatchResiduesMover |
| NcontactsCalculator.cc | |
| NcontactsCalculator.hh | Header file for NcontactsCalculator class |
| SheetConstraintsRCG.cc | |
| SheetConstraintsRCG.fwd.hh | |
| SheetConstraintsRCG.hh | |
| SheetCstGeneratorCreator.hh | This class will create instances of the SheetConstraintsRCG mover |
| ► flexpack | |
| ► annealer | |
| FlexbbSimAnnealer.cc | Annealer for optimizing both backbone and sidechain conformations implementation |
| FlexbbSimAnnealer.fwd.hh | Forward declarations and typedefs for the FlexbbSimAnnealer class |
| FlexbbSimAnnealer.hh | |
| ► interaction_graph | |
| FlexbbIGFactory.cc | |
| FlexbbIGFactory.fwd.hh | |
| FlexbbIGFactory.hh | |
| FlexbbInteractionGraph.cc | |
| FlexbbInteractionGraph.fwd.hh | Forward declaration of base-class FlexbbIG and associated typedefs |
| FlexbbInteractionGraph.hh | |
| FlexbbSparseMatrixIndex.hh | Declaration of class for maintaining sparse matrix indices for flexbb states |
| MinimalistFlexbbInteractionGraph.cc | Class implementation for minimimalist on-the-fly RPE calculating FlexbbInteractionGraph |
| MinimalistFlexbbInteractionGraph.fwd.hh | Class forward declaration for minimimalist on-the-fly RPE calculating FlexbbInteractionGraph |
| MinimalistFlexbbInteractionGraph.hh | Class declaration for minimimalist on-the-fly RPE calculating FlexbbInteractionGraph |
| OTFFlexbbInteractionGraph.cc | Class implementation for OTF flexbb IG |
| OTFFlexbbInteractionGraph.fwd.hh | |
| OTFFlexbbInteractionGraph.hh | |
| PrecomputedFlexbbInteractionGraph.cc | |
| PrecomputedFlexbbInteractionGraph.fwd.hh | |
| PrecomputedFlexbbInteractionGraph.hh | |
| ► rotamer_set | |
| FlexbbRotamerSet.cc | |
| FlexbbRotamerSet.fwd.hh | |
| FlexbbRotamerSet.hh | Declaration for a class to hold rotamers for a single backbone conformation in a flexible packing run |
| FlexbbRotamerSets.cc | |
| FlexbbRotamerSets.fwd.hh | |
| FlexbbRotamerSets.hh | Declaration for a class to hold a set of rotamers for a flexible packing run |
| FlexPacker.cc | |
| FlexPacker.fwd.hh | |
| FlexPacker.hh | |
| OtherContextScoreFunction.cc | |
| OtherContextScoreFunction.hh | |
| ► flexpep_docking | |
| FlexPepDockingAbInitio.cc | |
| FlexPepDockingAbInitio.fwd.hh | |
| FlexPepDockingAbInitio.hh | Low-resolution part of docking protocol |
| FlexPepDockingFlags.cc | Flags structure for FlexPepDocking protocols |
| FlexPepDockingFlags.fwd.hh | Flags structure for FlexPepDocking protocols - forward declarations |
| FlexPepDockingFlags.hh | Flags structure for FlexPepDocking protocols |
| FlexPepDockingLowRes.cc | |
| FlexPepDockingLowRes.fwd.hh | |
| FlexPepDockingLowRes.hh | Low-resolution part of docking protocol |
| FlexPepDockingPoseMetrics.cc | Metrics calculations specific for FlexPepDock (at least for now) |
| FlexPepDockingPoseMetrics.fwd.hh | |
| FlexPepDockingPoseMetrics.hh | Metrics calculations specific for FlexPepDock (at least for now) |
| FlexPepDockingProtocol.cc | Protocol for docking flexible peptides onto globular proteins |
| FlexPepDockingProtocol.hh | Protocol for docking flexible peptides onto globular proteins |
| FlexPepDockingProtocolCreator.hh | |
| ► floppy_tail | |
| FloppyTail_publication.cc | FloppyTail extra functions from original publication - this calculates some statistics used for the first published use of the code (Kleiger G, Saha A, Lewis S, Kuhlman B, Deshaies RJ. Rapid E2-E3 assembly and disassembly enable processive ubiquitylation of cullin-RING ubiquitin ligase substrates. Cell. 2009 Nov 25;139(5):957-68. PubMed PMID: 19945379.) |
| FloppyTail_publication.hh | FloppyTail extra functions from original publication - this calculates some statistics used for the first published use of the code (Kleiger G, Saha A, Lewis S, Kuhlman B, Deshaies RJ. Rapid E2-E3 assembly and disassembly enable processive ubiquitylation of cullin-RING ubiquitin ligase substrates. Cell. 2009 Nov 25;139(5):957-68. PubMed PMID: 19945379.) |
| FloppyTailMover.cc | This app was initially intended for modeling the binding of a long unstructured C-terminal tail to some other part of a protein. It now works for N-terminal, C-terminal, and internal flexible regions. It works best as a method for sampling space to see what is possible, preferably in conjunction with extensive experimental constraints. It is not meant to produce ab-initio style models of folded complexes |
| FloppyTailMover.fwd.hh | FloppyTail forward declaration |
| FloppyTailMover.hh | FloppyTail headers |
| ► flxbb | |
| DesignTask.cc | |
| DesignTask.fwd.hh | |
| DesignTask.hh | |
| FilterStructs.cc | |
| FilterStructs.fwd.hh | |
| FilterStructs.hh | Filter structures |
| FlxbbDesign.cc | Perform cycles of design and relax with filter |
| FlxbbDesign.fwd.hh | Perform cycles of design and relax with filter |
| FlxbbDesign.hh | Perform cycles of design and relax with filter |
| FlxbbDesign_main.cc | |
| FlxbbDesign_main.hh | |
| FlxbbDesignCreator.hh | |
| InterlockAroma.cc | Place interlocking aromatic residues |
| InterlockAroma.fwd.hh | |
| InterlockAroma.hh | Perform cycles of design and relax with filter |
| InterlockAromaCreator.hh | This class will create instances of Mover InterlockAroma for the MoverFactory |
| LayerDesignOperation.cc | Design residues with selected amino acids depending on the enviroment: layer. The layer of each residue is assigned as core, boundary, or surface, which are defined by accessible surface of mainchain + CB. If resfile is read before calling this operation, this operation is not applied for the residues defined by PIKAA |
| LayerDesignOperation.fwd.hh | |
| LayerDesignOperation.hh | Design residues with selected amino acids depending on the enviroment: layer. The layer of each residue is assigned as core, boundary, or surface, which are defined by accessible surface of mainchain + CB. If resfile is read before calling this operation, this operation is not applied for the residues defined by PIKAA |
| LayerDesignOperationCreator.hh | |
| utility.cc | |
| utility.hh | |
| ► forge | |
| ► build | |
| Bridge.cc | Connect two contiguous but disjoint sections of a Pose into one continuous section |
| Bridge.fwd.hh | Forward declaration for Bridge |
| Bridge.hh | Connect two contiguous but disjoint sections of a Pose into one continuous section |
| BuildInstruction.cc | |
| BuildInstruction.fwd.hh | Forward declaration for BuildInstruction |
| BuildInstruction.hh | Tracks modifications to be made and is capable of residue length changes on a Pose |
| BuildManager.cc | |
| BuildManager.fwd.hh | Forward declaration for BuildManager |
| BuildManager.hh | Container for managing BuildInstructions |
| ConnectRight.cc | Instruction to connect one Pose onto the right side of another |
| ConnectRight.fwd.hh | Forward declaration for ConnectRight |
| ConnectRight.hh | Instruction to connect one Pose onto the right side of another |
| GrowLeft.cc | Instruction to create an n-side extension |
| GrowLeft.fwd.hh | Forward declaration for GrowLeft |
| GrowLeft.hh | Instruction to create an n-side extension |
| GrowRight.cc | Instruction to create a c-side extension |
| GrowRight.fwd.hh | Forward declaration for GrowRight |
| GrowRight.hh | Instruction to create a c-side extension |
| Interval.fwd.hh | Forward declaration for Interval |
| Interval.hh | |
| RelativeConnectRight.cc | Version of ConnectRight instruction that depends upon results from another BuildInstruction |
| RelativeConnectRight.fwd.hh | Forward declaration for RelativeConnectRight |
| RelativeConnectRight.hh | Version of ConnectRight instruction that depends upon results from another BuildInstruction |
| RelativeSequencePosition.fwd.hh | Forward declaration for RelativeSequencePosition |
| RelativeSequencePosition.hh | Function objects to compute relative positions for RelativeConnectRight |
| SegmentInsert.cc | Insert an external segment flanked by new regions |
| SegmentInsert.fwd.hh | Forward declaration for SegmentInsert |
| SegmentInsert.hh | Insert an external segment flanked by new regions |
| SegmentRebuild.cc | Instruction to rebuild a segment |
| SegmentRebuild.fwd.hh | Forward declaration for SegmentRebuild |
| SegmentRebuild.hh | Instruction to rebuild a segment |
| SegmentSwap.cc | Instruction to swap a segment with an external segment |
| SegmentSwap.fwd.hh | Forward declaration for SegmentSwap |
| SegmentSwap.hh | Instruction to swap a segment with an external segment |
| ► components | |
| BDR.cc | |
| BDR.fwd.hh | Forward declaration for BDR |
| BDR.hh | |
| BDRSegmentInfo.fwd.hh | Forward declaration for BDRSegmentInfo |
| BDRSegmentInfo.hh | |
| VarLengthBuild.cc | Component that performs a simplified version of a protocol for variable length remodeling of protein backbone segments |
| VarLengthBuild.fwd.hh | Forward declaration for protocols::forge::components::VarLengthBuild |
| VarLengthBuild.hh | |
| ► constraints | |
| ConstraintFileCstGeneratorCreator.hh | This class will create instances of the ConstraintFileRCG mover |
| ConstraintFileRCG.cc | |
| ConstraintFileRCG.fwd.hh | |
| ConstraintFileRCG.hh | |
| InverseRotamersCstGeneratorCreator.hh | This class will create instances of the InverseRotamersRCG mover |
| InverseRotamersRCG.cc | |
| InverseRotamersRCG.fwd.hh | |
| InverseRotamersRCG.hh | |
| InvrotTreeCstGeneratorCreator.hh | This class will create instances of the InvrotTreeRCG mover |
| InvrotTreeRCG.cc | |
| InvrotTreeRCG.fwd.hh | |
| InvrotTreeRCG.hh | |
| NtoC_RCG.cc | |
| NtoC_RCG.fwd.hh | |
| NtoC_RCG.hh | |
| NtoCCstGeneratorCreator.hh | This class will create instances of the NtoC_RCG mover |
| RemoveCsts.cc | |
| RemoveCsts.hh | |
| RemoveCstsCreator.hh | This class will create instances of the RemoveCsts mover |
| ► methods | |
| chainbreak_eval.cc | Methods for chainbreak evaluation |
| chainbreak_eval.hh | Methods for chainbreak evaluation |
| fold_tree_functions.cc | Methods for manipulating FoldTrees |
| fold_tree_functions.hh | Methods for manipulating FoldTrees |
| fragment_functions.cc | Methods for manipulating fragments |
| fragment_functions.hh | Methods for manipulating fragments |
| pose_mod.cc | Methods for Pose modifications |
| pose_mod.hh | Methods for Pose modifications |
| util.cc | Miscellaneous utility functions for forge |
| util.hh | Miscellaneous utility functions for forge |
| ► remodel | |
| RemodelAccumulator.cc | |
| RemodelAccumulator.hh | |
| RemodelConstraintGenerator.cc | |
| RemodelConstraintGenerator.fwd.hh | |
| RemodelConstraintGenerator.hh | Abstract base class that generates constraints during forge loop remodelling |
| RemodelData.cc | |
| RemodelData.hh | |
| RemodelDesignMover.cc | |
| RemodelDesignMover.hh | |
| RemodelEnzdesCstModule.cc | |
| RemodelEnzdesCstModule.fwd.hh | |
| RemodelEnzdesCstModule.hh | This file handles merging constraint defined by enzdes type cstfile |
| RemodelGlobalFrame.cc | |
| RemodelGlobalFrame.fwd.hh | |
| RemodelGlobalFrame.hh | |
| RemodelLoopMover.cc | Loop modeling protocol based on routines from Remodel and EpiGraft packages in Rosetta++ |
| RemodelLoopMover.fwd.hh | Forward declaration for RemodelLoopMover |
| RemodelLoopMover.hh | Loop modeling protocol based on routines from Remodel and EpiGraft packages in Rosetta++ |
| RemodelLoopMoverCreator.hh | This class will create instances of Mover RemodelLoopMover for the MoverFactory |
| RemodelMover.cc | |
| RemodelMover.fwd.hh | |
| RemodelMover.hh | |
| RemodelMoverCreator.hh | |
| RemodelRotamerLinks.cc | |
| RemodelRotamerLinks.fwd.hh | |
| RemodelRotamerLinks.hh | When operated on a PackerTask, adds RotamerLinks to it that will |
| RemodelRotamerLinksCreator.hh | |
| RemodelWorkingSet.cc | |
| RemodelWorkingSet.hh | |
| ResidueVicinityCstGeneratorCreator.hh | This class will create instances of the ResidueVicinityRCG mover |
| ResidueVicinityRCG.cc | |
| ResidueVicinityRCG.hh | |
| ► frag_picker | |
| ► nonlocal | |
| NonlocalFrags.cc | |
| NonlocalFrags.fwd.hh | |
| NonlocalFrags.hh | |
| NonlocalFragsMain.cc | |
| NonlocalFragsMain.hh | |
| NonlocalPair.fwd.hh | Forward declaration for NonlocalPair |
| NonlocalPair.hh | Nonlocal fragment pair |
| ► quota | |
| ABEGO_SS_Config.cc | |
| ABEGO_SS_Config.hh | Reads a config file for quota selector |
| ABEGO_SS_Map.cc | Map ABEGO vs. SS combinations |
| ABEGO_SS_Map.fwd.hh | |
| ABEGO_SS_Map.hh | Class for a quota pool based on secondary structure prediction and ABEGO torsion bin classification |
| ABEGO_SS_Pool.cc | |
| ABEGO_SS_Pool.fwd.hh | Class for a quota pool based on secondary structure prediction and ABEGO torsion bin classification |
| ABEGO_SS_Pool.hh | Quota selector based on difefrent secondary structure predicitons |
| QuotaCollector.cc | |
| QuotaCollector.fwd.hh | Forward declaration for QuotaCollector |
| QuotaCollector.hh | Pure virtual base class for a container holding fragment candidates |
| QuotaConfig.cc | |
| QuotaConfig.hh | Reads a config file for quota selector |
| QuotaPool.fwd.hh | Base class for a quota pool |
| QuotaPool.hh | Single pool used by quota |
| QuotaSelector.cc | |
| QuotaSelector.fwd.hh | |
| QuotaSelector.hh | Selector that picks best fragments based on their total score |
| SecondaryStructurePool.cc | |
| SecondaryStructurePool.fwd.hh | Class for a quota pool based on secondary structure prediction |
| SecondaryStructurePool.hh | Quota selector based on difefrent secondary structure predicitons |
| TorsionBinPool.cc | |
| TorsionBinPool.hh | Quota selector based on torsion bin prediciton |
| ► scores | |
| ABEGO_SS_Score.cc | Scores a fragment by secondary structure similarity |
| ABEGO_SS_Score.hh | Scores a fragment by secondary structure similarity |
| AdaptiveScoreHistogram.cc | |
| AdaptiveScoreHistogram.fwd.hh | AdaptiveScoreHistogram forward declaration |
| AdaptiveScoreHistogram.hh | A very basic histogram to keep statistics of scores |
| AmbigCSScore.cc | Object that scores a fragment by target-observed/vall-predicted chemical shift distances |
| AmbigCSScore.hh | Object that scores a fragment by its crmsd to the native |
| AtomBasedConstraintsScore.cc | |
| AtomBasedConstraintsScore.fwd.hh | AtomBasedConstraintsScore forward declaration |
| AtomBasedConstraintsScore.hh | |
| AtomPairConstraintsScore.cc | |
| AtomPairConstraintsScore.fwd.hh | |
| AtomPairConstraintsScore.hh | |
| BFactor.cc | Base class for fragment scoring |
| BFactor.hh | Base class for fragment scoring |
| CachingScoringMethod.hh | Adds cashing functionality to a FragmentScoringMethod object |
| ConstScore.hh | Score that adds a constant (so basically it does nothing!) |
| CSScore.cc | Object that scores a fragment by target-observed/vall-predicted chemical shift distances |
| CSScore.hh | Object that scores a fragment by its crmsd to the native |
| DihedralConstraintsScore.cc | Calculates a score based on how close are dihdral angles in a Vall chunk to their target values |
| DihedralConstraintsScore.fwd.hh | DihedralConstraintsScore forward declaration |
| DihedralConstraintsScore.hh | |
| DisulfideDistance.cc | |
| DisulfideDistance.hh | |
| DisulfideIdentity.cc | Base class for fragment scoring |
| DisulfideIdentity.hh | Base class for fragment scoring |
| FourAtomsConstraintData.cc | |
| FourAtomsConstraintData.fwd.hh | |
| FourAtomsConstraintData.hh | Holder for data necessary to create a single constraint based on four atoms |
| fragment_scoring_utilities.cc | |
| fragment_scoring_utilities.hh | Functions and data types common for fragment scoring |
| FragmentAllAtomCrmsd.cc | Object that scores a fragment by its crmsd to the native |
| FragmentAllAtomCrmsd.hh | Object that scores a fragment by its crmsd to the native |
| FragmentChunkCrms.cc | |
| FragmentChunkCrms.hh | Object that scores a fragment by its tmscore to the native |
| FragmentCrmsd.cc | Scores fragments by disulfide-linke Calpha distances |
| FragmentCrmsd.hh | Object that scores a fragment by its crmsd to the native |
| FragmentCrmsdResDepth.cc | Object that scores a fragment by its crmsd to the native |
| FragmentCrmsdResDepth.hh | Object that scores a fragment by its crmsd and residue depth to the native |
| FragmentDME.cc | Object that scores a fragment by its Distance Matrix Error (DME) to the native |
| FragmentDME.hh | Object that scores a fragment by its Distance Matrix Error (DME) to the native |
| FragmentScoreManager.cc | |
| FragmentScoreManager.fwd.hh | FragmentScoreManager forward declaration |
| FragmentScoreManager.hh | FragmentScoreManager forward declaration |
| FragmentScoreMap.fwd.hh | FragmentScoreMap forward declaration |
| FragmentScoreMap.hh | |
| FragmentScoringMethod.fwd.hh | |
| FragmentScoringMethod.hh | FragmentScoringMethod forward declaration |
| GunnCost.cc | |
| GunnCost.hh | |
| GunnCostScore.cc | Object that scores a fragment by its crmsd to the native |
| GunnCostScore.hh | Object that scores a fragment by Gunn cost function (how it fits to the local structure) |
| HydrophobicityProfileSimilarity.cc | Base class for fragment scoring |
| HydrophobicityProfileSimilarity.hh | Object that scores a fragment by hydrophobicity |
| HydrophobicitySimilarity.cc | Base class for fragment scoring |
| HydrophobicitySimilarity.hh | Object that scores a fragment by hydrophobicity |
| InterbondAngleScore.cc | |
| InterbondAngleScore.fwd.hh | |
| InterbondAngleScore.hh | |
| JCoupling.cc | |
| JCoupling.hh | |
| LAMBEGO_Similarity.cc | |
| LAMBEGO_Similarity.hh | |
| MidPhiOut.cc | |
| MidPhiOut.hh | Scores fragments by disulfide-linke Calpha distances |
| MidPsiOut.cc | |
| MidPsiOut.hh | Object that scores a fragment by its crmsd to the native |
| PartialSecondarySimilarity.cc | Scores a fragment by secondary structure similarity but throws out the worst 20% of the residue matches |
| PartialSecondarySimilarity.hh | |
| PCS_FragDistance.cc | |
| PCS_FragDistance.hh | |
| Phi.cc | Base class for fragment scoring |
| Phi.hh | Object that scores a fragment by predicted Phi torsions |
| PhiPsiRmsd.cc | |
| PhiPsiRmsd.hh | Object that scores a fragment by its crmsd to the native |
| PhiPsiSquareWell.cc | |
| PhiPsiSquareWell.hh | |
| ProfileScore.cc | Scores a fragment by an amino acid sequence identity |
| ProfileScore.fwd.hh | |
| ProfileScore.hh | FragmentScoringMethod forward declaration |
| ProfileScoreBlosum62.cc | |
| ProfileScoreBlosum62.hh | |
| ProfileScoreDistWeight.cc | |
| ProfileScoreDistWeight.hh | |
| ProfileScoreL1.cc | |
| ProfileScoreL1.hh | |
| ProfileScoreStructL1.cc | Scores a fragment using structure based profiles |
| ProfileScoreStructL1.hh | Scores a fragment by L1 structure based profile score |
| ProfileScoreSubMatrix.cc | Scores a fragment by substitution matrix (e.g. Blosum62) profile score |
| ProfileScoreSubMatrix.hh | Scores a fragment by substitution matrix (e.g. Blosum62) profile score |
| ProlinePhiScore.cc | |
| ProlinePhiScore.hh | Base class for fragment scoring |
| Psi.cc | Base class for fragment scoring |
| Psi.hh | Object that scores a fragment by predicted Psi torsions |
| PValuedFragmentScoreManager.cc | |
| PValuedFragmentScoreManager.hh | Score manager that stores statistics of all scores. This allows estimate p-value for a score |
| RamaScore.cc | |
| RamaScore.hh | Base class for fragment scoring |
| RDCScore.cc | Object that scores a fragment by its RDC |
| RDCScore.hh | Object that scores a fragment by its crmsd to the native |
| RDCScore_Gront.cc | |
| RDCScore_Gront.fwd.hh | |
| RDCScore_Gront.hh | |
| ScoreEValuator.cc | Scores a fragment by an amino acid sequence identity |
| ScoreEValuator.hh | Object that scores a fragment by its crmsd to the native |
| SecondaryIdentity.cc | Scores a fragment by an amino acid sequence identity |
| SecondaryIdentity.hh | Scores a fragment by an amino acid sequence identity |
| SecondarySimilarity.cc | Scores a fragment by secondary structure similarity |
| SecondarySimilarity.hh | Scores a fragment by secondary structure similarity |
| SequenceIdentity.cc | Base class for fragment scoring |
| SequenceIdentity.hh | Base class for fragment scoring |
| SolventAccessibility.cc | Base class for fragment scoring |
| SolventAccessibility.hh | Object that scores a fragment by predicted solvent accessibility |
| TalosSSSimilarity.cc | Scores a fragment by secondary structure similarity |
| TalosSSSimilarity.hh | Scores a fragment by secondary structure similarity |
| TorsionBinSimilarity.cc | |
| TorsionBinSimilarity.hh | |
| BestTotalScoreSelector.cc | |
| BestTotalScoreSelector.fwd.hh | |
| BestTotalScoreSelector.hh | Selector that picks best fragments based on their total score |
| BoundedCollector.fwd.hh | |
| BoundedCollector.hh | |
| BoundedPriorityQueue.hh | |
| CandidatesCollector.fwd.hh | Forward declaration for CandidatesCollector |
| CandidatesCollector.hh | Pure virtual base class for a container holding fragment candidates |
| CommonFragmentComparators.fwd.hh | Few ways to compare fragment candidates (forward definitions) |
| CommonFragmentComparators.hh | Few ways to compare fragment candidates |
| CompositeFragmentSelector.cc | Selector that picks best fragments based on their total score |
| CompositeFragmentSelector.hh | Selector that picks best fragments based on their total score |
| Contact.fwd.hh | |
| Contact.hh | A contact |
| ContactCounts.fwd.hh | |
| ContactCounts.hh | Contact counts |
| ContactTypes.cc | Fragment picker contact types |
| ContactTypes.hh | Fragment picker type declarations |
| CS2ndShift.cc | |
| CS2ndShift.hh | |
| CSTalosIO.cc | |
| CSTalosIO.hh | Class that converts Talos object into secondary shifts list |
| CustomScoreSelector.cc | |
| CustomScoreSelector.fwd.hh | |
| CustomScoreSelector.hh | Selector that picks best fragments based on their total score |
| DiversifyCrmsdByClustering.cc | |
| DiversifyCrmsdByClustering.hh | Selector that picks fragments diversified by crmsd (by means of hierarchical clustering) |
| DiversifyCrmsdSelector.cc | |
| DiversifyCrmsdSelector.hh | Selector that picks best fragments based on their total score |
| DiversifyDihedralsSelector.cc | |
| DiversifyDihedralsSelector.hh | Selector that picks best fragments based on their total score |
| Faraggi_SA.cc | Faraggi maximum SA values from Faraggi et al. Proteins 2008 |
| Faraggi_SA.hh | Faraggi maximum SA values from Faraggi et al. Proteins 2008 |
| FragmentCandidate.cc | |
| FragmentCandidate.fwd.hh | |
| FragmentCandidate.hh | Something that might become a fragment if its scores will be good enough |
| FragmentComparatorBase.fwd.hh | |
| FragmentComparatorBase.hh | Defines a base class for all fragment comparators |
| FragmentPicker.cc | Fragment picker - the core part of picking machinery |
| FragmentPicker.fwd.hh | Fragment picker - forward declaration |
| FragmentPicker.hh | Fragment picker - the core part of picking machinery |
| FragmentSelectingRule.fwd.hh | |
| FragmentSelectingRule.hh | Selector that picks best fragments based on their total score |
| GrabAllCollector.hh | |
| JCouplingIO.cc | |
| JCouplingIO.hh | |
| LAMBEGO_IO.cc | |
| LAMBEGO_IO.hh | Reader for a probability distribution over A,B,E,G,O torsion bins |
| LazySortedVector1.hh | |
| PdbIdChunkFilter.cc | |
| PdbIdChunkFilter.fwd.hh | |
| PdbIdChunkFilter.hh | |
| PhiPsiTalosIO.cc | |
| PhiPsiTalosIO.hh | Class that reads and writes Phi-Psi in TALOS format |
| SidechainContactDistCutoff.cc | Defines sidechain contact distance cutoffs |
| SidechainContactDistCutoff.fwd.hh | |
| SidechainContactDistCutoff.hh | Defines sidechain contact distance cutoffs |
| TorsionBinIO.cc | |
| TorsionBinIO.hh | Reader for a probability distribution over A,B,E,G,O torsion bins |
| VallChunk.cc | Contiguous chunk of residues taken from a vall |
| VallChunk.fwd.hh | Forward declaration for VallChunk |
| VallChunk.hh | Contiguous chunk of residues taken from a vall |
| VallChunkFilter.fwd.hh | Forward declaration for VallChunkFilter |
| VallChunkFilter.hh | Defines two basic chunk filters based on pdb id |
| VallProvider.cc | Reads a vall library and serves the data in chunks |
| VallProvider.fwd.hh | Forward declaration for VallProvider |
| VallProvider.hh | Reads a vall library and serves the data in chunks |
| VallResidue.cc | Class for managing a line of the Vall fragment library |
| VallResidue.fwd.hh | Forward declaration for core::fragment::picking::vall:VallResidue |
| VallResidue.hh | Class for managing a line of the Vall fragment library |
| ► frags | |
| heap.cc | |
| heap.hh | |
| RMSVallData.hh | |
| TorsionFragment.cc | |
| TorsionFragment.fwd.hh | |
| TorsionFragment.hh | |
| VallData.cc | |
| VallData.fwd.hh | |
| VallData.hh | |
| ► genetic_algorithm | |
| Entity.cc | |
| Entity.fwd.hh | |
| Entity.hh | Unit employed/optimized by GeneticAlgorithm |
| EntityRandomizer.cc | |
| EntityRandomizer.fwd.hh | Fowrad declaration of the class that controls the alteration of the traits that define an Entity |
| EntityRandomizer.hh | Controls the alteration of the traits that define Entity |
| FitnessFunction.hh | Determines the fitness of Entity for GeneticAlgorithm |
| GeneticAlgorithm.cc | |
| GeneticAlgorithm.fwd.hh | |
| GeneticAlgorithm.hh | Template class for genetic algorithm protocols |
| Mutate1Randomizer.cc | Class to mutate only a single position at a time in any given entity |
| Mutate1Randomizer.fwd.hh | Fowrad declaration of the class that controls the alteration of the traits that define an Entity |
| Mutate1Randomizer.hh | Class to mutate only a single position at a time in any given entity |
| ► grafting | |
| AnchoredGraftMover.cc | Method definitions for AnchoredGraftMover |
| AnchoredGraftMover.fwd.hh | |
| AnchoredGraftMover.hh | Class to graft a piece into a pose. Jared Adolf-Bryfogle (jadol.nosp@m.fbr@.nosp@m.gmail.nosp@m..com) |
| GraftMoverBase.cc | Base class for GraftMovers |
| GraftMoverBase.fwd.hh | Forward declarations for GraftMoverBase class |
| GraftMoverBase.hh | Base class for graftmovers |
| util.cc | Utility functions for grafting |
| util.hh | Header for grafting utility functions |
| ► hotspot_hashing | |
| ► movers | |
| PlaceProbeMover.cc | |
| PlaceProbeMover.hh | |
| PlaceSurfaceProbe.cc | |
| PlaceSurfaceProbe.fwd.hh | |
| PlaceSurfaceProbe.hh | |
| PlaceSurfaceProbeCreator.hh | |
| HotspotStub.cc | |
| HotspotStub.fwd.hh | |
| HotspotStub.hh | |
| HotspotStubSet.cc | |
| HotspotStubSet.fwd.hh | |
| HotspotStubSet.hh | |
| SearchPattern.cc | |
| SearchPattern.fwd.hh | |
| SearchPattern.hh | |
| SearchPatternRotSetOp.cc | Creates rigid body variants from search pattern during repacking |
| SearchPatternRotSetOp.fwd.hh | |
| SearchPatternRotSetOp.hh | Creates rigid body variants from search pattern during repacking |
| SICSearchPattern.cc | |
| SICSearchPattern.hh | |
| StubGenerator.cc | |
| StubGenerator.fwd.hh | |
| StubGenerator.hh | |
| SurfaceSearchPattern.cc | |
| SurfaceSearchPattern.hh | |
| ► hybridization | |
| AllResiduesChanged.hh | |
| CartesianHybridize.cc | |
| CartesianHybridize.fwd.hh | |
| CartesianHybridize.hh | |
| CartesianHybridizeCreator.hh | |
| CartesianSampler.cc | |
| CartesianSampler.fwd.hh | |
| CartesianSampler.hh | |
| ChunkTrialMover.cc | Wrapper for InsertChunkMover. It can take a random template and steal coordinates of all chunks or a random one |
| ChunkTrialMover.fwd.hh | |
| ChunkTrialMover.hh | Wrapper for InsertChunkMover. It can take a random template and steal coordinates of all chunks or a random one |
| DDomainParse.cc | A reimplementation of DDomain domain parsing algorithm, Protein Sci.16,947–955 (2007) |
| DDomainParse.hh | A reimplementation of DDomain domain parsing algorithm, Protein Sci.16,947–955 (2007) |
| DomainAssembly.cc | Domain Assembly |
| DomainAssembly.fwd.hh | |
| DomainAssembly.hh | |
| FoldTreeHybridize.cc | Align a random jump to template |
| FoldTreeHybridize.fwd.hh | |
| FoldTreeHybridize.hh | Align a random jump to template |
| FoldTreeHybridizeCreator.hh | |
| HybridizeFoldtreeDynamic.cc | A mover to dynamically manipulate fold tree during the template hybridization sampling |
| HybridizeFoldtreeDynamic.fwd.hh | |
| HybridizeFoldtreeDynamic.hh | |
| HybridizeProtocol.cc | |
| HybridizeProtocol.fwd.hh | |
| HybridizeProtocol.hh | Add constraints to the current pose conformation |
| HybridizeProtocolCreator.hh | |
| HybridizeSetup.cc | |
| HybridizeSetup.fwd.hh | |
| HybridizeSetup.hh | Add constraints to the current pose conformation |
| HybridizeSetupMoverCreator.hh | |
| InsertChunkMover.cc | Align a random jump to template |
| InsertChunkMover.hh | Align a random jump to template |
| MRMover.cc | |
| MRMover.hh | |
| TemplateHistory.cc | |
| TemplateHistory.fwd.hh | |
| TemplateHistory.hh | |
| TMalign.hh | A reimplementation of TM-align algorithm |
| util.cc | Align a random jump to template |
| util.hh | Align a random jump to template |
| WeightedFragmentSmoothTrialMover.cc | Fragment insertion and trial, each residue has a customized weight for the frequency of insertion |
| WeightedFragmentSmoothTrialMover.fwd.hh | |
| WeightedFragmentSmoothTrialMover.hh | Fragment insertion and trial, each residue has a customized weight for the frequency of insertion |
| WeightedFragmentTrialMover.cc | Fragment insertion and trial, each residue has a customized weight for the frequency of insertion |
| WeightedFragmentTrialMover.fwd.hh | |
| WeightedFragmentTrialMover.hh | Fragment insertion and trial, each residue has a customized weight for the frequency of insertion |
| ► idealize | |
| idealize.cc | |
| idealize.hh | Protocols for idealizing a Pose |
| IdealizeMover.cc | |
| IdealizeMover.fwd.hh | Protocols for idealizing a Pose |
| IdealizeMover.hh | Protocols for idealizing a Pose |
| IdealizeMoverCreator.hh | |
| ► init | |
| init.cc | Declare WidgetRegistrators as static (global) variables in this .cc file so that at load time, they will be initialized, and the Creator classes they register will be handed to the appropriate WidgetFactory |
| init.hh | Initialization function to ensure all load-time factory registration occurs for classes that live in the protocols library. protocols::init::init() calls core::init::init(), and devel::init() call protocols::init::init() |
| ► inputter | |
| FastaInputter.cc | An inputter that takes a list of fasta |
| FastaInputter.fwd.hh | An inputter that takes a list of fasta |
| FastaInputter.hh | An inputter that takes a list of fastas |
| Inputter.cc | |
| Inputter.fwd.hh | An inputter, a class that returns a poseSP |
| Inputter.hh | An inputter, a class that returns a poseSP |
| InputterStream.cc | InputterStream holds a list of of streams and does VERY basic things with them like controls whether structures are duplicated across masters and controls whether to take the list sequentially or round robin |
| InputterStream.fwd.hh | InputterStream holds a list of of streams and does VERY basic things with them like controls whether structures are duplicated across masters and controls whether to take the list sequentially or round robin |
| InputterStream.hh | InputterStream holds a list of of streams and does VERY basic things with them like controls whether structures are duplicated across masters and controls whether to take the list sequentially or round robin |
| PDBInputter.cc | An inputter that takes a list of pdbs |
| PDBInputter.fwd.hh | An inputter that takes a list of pdbs |
| PDBInputter.hh | An inputter that takes a list of pdbs |
| SilentFileInputter.cc | An inputter that takes a list of silent files |
| SilentFileInputter.fwd.hh | An inputter that takes a list of silent files |
| SilentFileInputter.hh | An inputter that takes a list of silent files |
| ► jd2 | |
| ► archive | |
| ArchiveBase.cc | |
| ArchiveBase.fwd.hh | |
| ArchiveBase.hh | |
| ArchiveManager.cc | |
| ArchiveManager.fwd.hh | |
| ArchiveManager.hh | |
| ArchiveMasterBase.cc | |
| ArchiveMasterBase.hh | |
| EvaluatedArchive.cc | |
| EvaluatedArchive.hh | |
| MPIArchiveJobDistributor.cc | |
| MPIArchiveJobDistributor.fwd.hh | |
| MPIArchiveJobDistributor.hh | |
| NormalizedEvaluatedArchive.cc | |
| NormalizedEvaluatedArchive.hh | |
| VarianceStatisticsArchive.cc | |
| VarianceStatisticsArchive.fwd.hh | |
| VarianceStatisticsArchive.hh | |
| ► parser | |
| BluePrint.cc | |
| BluePrint.fwd.hh | |
| BluePrint.hh | |
| DataLoader.cc | Implementation of the XML parser's DataLoader base class (ctor & dstor) |
| DataLoader.fwd.hh | Forward declartion of the XML parser's DataLoader class |
| DataLoader.hh | Declartion of the XML parser's DataLoader class |
| DataLoaderCreator.cc | Creator class for the parser's DataLoader classes |
| DataLoaderCreator.hh | Creator class for the parser's DataLoader classes |
| DataLoaderFactory.cc | Implementation of the factory class for the parser's DataLoader classes |
| DataLoaderFactory.hh | Factory class for the parser's DataLoader classes |
| FragmentReader.cc | |
| FragmentReader.fwd.hh | |
| FragmentReader.hh | |
| FragSetLoader.cc | |
| FragSetLoader.hh | Declartion of the XML parser's FragSetLoader class for adding named FragSets to the basic::datacache::DataMap |
| MonteCarloLoader.cc | |
| MonteCarloLoader.hh | Declartion of the XML parser's MonteCarloLoader class for adding named ScoreFunctions to the basic::datacache::DataMap |
| ResidueSelectorLoader.cc | |
| ResidueSelectorLoader.hh | Declartion of the XML parser's ResidueSelectorLoader class for adding named ResidueSelectors to the basic::datacache::DataMap |
| ResidueSelectorLoaderCreator.hh | |
| ScoreFunctionLoader.cc | |
| ScoreFunctionLoader.hh | Declartion of the XML parser's ScoreFunctionLoader class for adding named ScoreFunctions to the basic::datacache::DataMap |
| StandardLoaderCreators.hh | |
| TaskOperationLoader.cc | |
| TaskOperationLoader.hh | Declartion of the XML parser's TaskOperationLoader class |
| AtomTreeDiffJobInputter.cc | |
| AtomTreeDiffJobInputter.fwd.hh | |
| AtomTreeDiffJobInputter.hh | Header file for AtomTreeDiffJobInputter class |
| AtomTreeDiffJobInputterCreator.hh | |
| AtomTreeDiffJobOutputter.cc | AtomTreeDiffJobOutputter |
| AtomTreeDiffJobOutputter.fwd.hh | Header file for AtomTreeDiffJobOutputter class, part of August 2008 job distributor as planned at RosettaCon08 |
| AtomTreeDiffJobOutputter.hh | Header file for AtomTreeDiffJobOutputter class |
| AtomTreeDiffJobOutputterCreator.hh | |
| BatchJobInputter.cc | |
| BatchJobInputter.fwd.hh | |
| BatchJobInputter.hh | Header file for BatchJobInputter class |
| BOINCJobDistributor.cc | Implementation of BOINCJobDistributor |
| BOINCJobDistributor.hh | Implementation of BOINCJobDistributor |
| FileJobOutputter.cc | August 2008 job distributor as planned at RosettaCon08 - FileJobOutputter |
| FileJobOutputter.fwd.hh | Header file for FileJobOutputter class, part of August 2008 job distributor as planned at RosettaCon08 |
| FileJobOutputter.hh | Header file for FileJobOutputter class, part of August 2008 job distributor as planned at RosettaCon08 |
| FileSystemJobDistributor.cc | August 2008 job distributor as planned at RosettaCon08 - Simplest class FileSystemJobDistributor |
| FileSystemJobDistributor.fwd.hh | August 2008 job distributor as planned at RosettaCon08 - Simplest class FileSystemJobDistributor |
| FileSystemJobDistributor.hh | August 2008 job distributor as planned at RosettaCon08 - Simplest class FileSystemJobDistributor |
| InnerJob.cc | |
| InnerJob.fwd.hh | Header file for InnerJob class, part of August 2008 job distributor as planned at RosettaCon08 |
| InnerJob.hh | Header file for Job classes, part of August 2008 job distributor as planned at RosettaCon08. This file is responsible for three ideas: "inner" jobs, "outer" jobs (with which the job distributor works) and job container (currently just typdefed in the .fwd.hh) |
| InnerMultiThreadingJob.cc | |
| InnerMultiThreadingJob.fwd.hh | Header file for Job classes, part of August 2008 job distributor as planned at RosettaCon08 |
| InnerMultiThreadingJob.hh | |
| JD2ResourceManager.cc | |
| JD2ResourceManager.fwd.hh | Forward header for the JD2ResourceManager |
| JD2ResourceManager.hh | |
| JD2ResourceManagerCreator.hh | |
| JD2ResourceManagerInputterCreator.hh | |
| JD2ResourceManagerJobInputter.cc | |
| JD2ResourceManagerJobInputter.hh | |
| JD2ResourceManagerJobInputterCreator.hh | |
| Job.cc | August 2008 job distributor as planned at RosettaCon08 - Job classes |
| Job.fwd.hh | Header file for Job classes, part of August 2008 job distributor as planned at RosettaCon08 |
| Job.hh | Header file for Job classes, part of August 2008 job distributor as planned at RosettaCon08. This file is responsible for three ideas: "inner" jobs, "outer" jobs (with which the job distributor works) and job container (currently just typdefed in the .fwd.hh) |
| JobDistributor.cc | August 2008 job distributor as planned at RosettaCon08 - Base class |
| JobDistributor.fwd.hh | August 2008 job distributor as planned at RosettaCon08 - Base class |
| JobDistributor.hh | |
| JobDistributorFactory.cc | |
| JobDistributorFactory.fwd.hh | |
| JobDistributorFactory.hh | |
| JobInputter.cc | August 2008 job distributor as planned at RosettaCon08 - Interface base class JobInputter |
| JobInputter.fwd.hh | Header file for JobInputter class, part of August 2008 job distributor as planned at RosettaCon08 |
| JobInputter.hh | Header file for JobInputter class, part of August 2008 job distributor as planned at RosettaCon08 |
| JobInputterCreator.cc | |
| JobInputterCreator.hh | Base class for JobInputterCreators for the JobInputter load-time factory registration scheme |
| JobInputterFactory.cc | JobInputterCreator base |
| JobInputterFactory.fwd.hh | JobInputterFactory forward header |
| JobInputterFactory.hh | JobInputterFactory |
| JobOutputter.cc | August 2008 job distributor as planned at RosettaCon08 - Base class JobOutputter |
| JobOutputter.fwd.hh | Header file for JobOutputter class, part of August 2008 job distributor as planned at RosettaCon08 |
| JobOutputter.hh | Header file for JobOutputter class, part of August 2008 job distributor as planned at RosettaCon08 |
| JobOutputterCreator.cc | |
| JobOutputterCreator.hh | Base class for JobOutputterCreators for the JobOutputter load-time factory registration scheme |
| JobOutputterFactory.cc | JobOutputterCreator base |
| JobOutputterFactory.fwd.hh | JobOutputterFactory forward header |
| JobOutputterFactory.hh | JobOutputterFactory |
| JobOutputterObserver.hh | Classes that want to add score_value pairs to poses before they are output should derive from this Observer class |
| LazySilentFileJobInputter.cc | |
| LazySilentFileJobInputter.fwd.hh | |
| LazySilentFileJobInputter.hh | |
| LazySilentFileJobInputterCreator.hh | |
| MpiFileBuffer.cc | |
| MpiFileBuffer.fwd.hh | |
| MpiFileBuffer.hh | Header file for MPISilentFileJobOutputter class, part of August 2008 job distributor as planned at RosettaCon08 this outputter will send silentstructs via MPI to dedicated node that will collect all structures |
| MPIFileBufJobDistributor.cc | Implementation of MPIFileBufJobDistributor |
| MPIFileBufJobDistributor.fwd.hh | |
| MPIFileBufJobDistributor.hh | |
| MPIMultiCommJobDistributor.cc | Implementation of MPIMultiCommJobDistributor |
| MPIMultiCommJobDistributor.fwd.hh | |
| MPIMultiCommJobDistributor.hh | |
| MPIWorkPartitionJobDistributor.cc | Implementation of MPIWorkPartitionJobDistributor - intended for MPI jobs on small numbers of nodes where the load can be balanced equally by the user |
| MPIWorkPartitionJobDistributor.fwd.hh | Forward header for MPIWorkPartitonJobDistributor |
| MPIWorkPartitionJobDistributor.hh | Header for MPIWorkPartitionJobDistributor - intended for MPI jobs on small numbers of nodes where the load can be balanced equally by the user |
| MPIWorkPoolJobDistributor.cc | Implementation of MPIWorkPoolJobDistributor |
| MPIWorkPoolJobDistributor.fwd.hh | Forward header for MPIWorkPoolJobDistributor |
| MPIWorkPoolJobDistributor.hh | Header for MPIWorkPoolJobDistributor - intended for continuous resamplig jobs that spawn new jobs based on a pool/archive of structures |
| MultiThreadingJob.cc | |
| MultiThreadingJob.fwd.hh | Header file for Job classes, part of August 2008 job distributor as planned at RosettaCon08 |
| MultiThreadingJob.hh | |
| NoOutputJobOutputter.hh | Header file for NoOutputJobOutputter class, part of August 2008 job distributor as planned at RosettaCon08 |
| NoOutputJobOutputterCreator.cc | NoOutputJobOutputCreator class, part of November 2011 XRW2 |
| NoOutputJobOutputterCreator.hh | |
| Parser.cc | August 2008 job distributor as planned at RosettaCon08 - Interface base class Parser |
| Parser.fwd.hh | Header file for Parser class, part of August 2008 job distributor |
| Parser.hh | Header file for Parser class, part of August 2008 job distributor |
| PDBJobInputter.cc | August 2008 job distributor as planned at RosettaCon08 - Base class PDBJobInputter |
| PDBJobInputter.fwd.hh | Header file for PDBJobInputter class, part of August 2008 job distributor as planned at RosettaCon08 |
| PDBJobInputter.hh | Header file for PDBJobInputter class, part of August 2008 job distributor as planned at RosettaCon08 |
| PDBJobInputterCreator.hh | |
| PDBJobOutputter.cc | August 2008 job distributor as planned at RosettaCon08 - PDBJobOutputter |
| PDBJobOutputter.fwd.hh | Header file for PDBJobOutputter class, part of August 2008 job distributor as planned at RosettaCon08 |
| PDBJobOutputter.hh | Header file for PDBJobOutputter class, part of August 2008 job distributor as planned at RosettaCon08 |
| PDBJobOutputterCreator.hh | |
| PoseInputStreamJobInputter.cc | |
| PoseInputStreamJobInputter.fwd.hh | |
| PoseInputStreamJobInputter.hh | Header file for PoseInputStreamJobInputter class |
| PoseInputStreamJobInputterCreator.hh | |
| ScoreMap.cc | A place to put some common functions for scoremap output |
| ScoreMap.hh | A place to put some common functions for scoremap output |
| ScoreOnlyJobOutputter.cc | |
| ScoreOnlyJobOutputter.fwd.hh | |
| ScoreOnlyJobOutputter.hh | |
| ScoreOnlyJobOutputterCreator.hh | |
| ScreeningJobInputter.cc | The ScreeningJobInputter The ScreeningJobInputter simplifies the process of inputting and handling input to a vHTS protocol. The ScreeningJobInputter takes in a JSON file using the -in:file:screening_job_file option This file is in the following format: { "jobs" : [ { "group_name" : "group_name_a", "proteins" : ["protein_a.pdb", "protein_b.pdb"], "ligands" : ["ligand_a.pdb", "ligand_b.pdb"] } ] "params : [ "aaa.param", "aab.param" |
| ScreeningJobInputter.fwd.hh | The ScreeningJobInputter forward headers |
| ScreeningJobInputter.hh | The ScreeningJobInputter forward headers |
| ScreeningJobInputterCreator.hh | Creator for ScreeningJobInputter |
| ShuffleJobDistributor.cc | |
| ShuffleJobDistributor.hh | Implementation of ShuffleFileSystemJobDistributor |
| SilentFileJobInputter.cc | |
| SilentFileJobInputter.fwd.hh | |
| SilentFileJobInputter.hh | Header file for SilentFileJobInputter class |
| SilentFileJobInputterCreator.hh | |
| SilentFileJobOutputter.cc | |
| SilentFileJobOutputter.fwd.hh | Header file for SilentFileJobOutputter class, part of August 2008 job distributor as planned at RosettaCon08 |
| SilentFileJobOutputter.hh | Header file for SilentFileJobOutputter class, part of August 2008 job distributor as planned at RosettaCon08 |
| SilentFileJobOutputterCreator.hh | |
| SingleFileBuffer.cc | |
| SingleFileBuffer.fwd.hh | |
| SingleFileBuffer.hh | |
| util.cc | |
| util.hh | August 2008 job distributor as planned at RosettaCon08 - Base class |
| ► jobdist | |
| JobDistributors.cc | |
| JobDistributors.fwd.hh | |
| JobDistributors.hh | |
| Jobs.cc | |
| Jobs.fwd.hh | Objects representing inputs for the JobDistributor |
| Jobs.hh | Objects representing inputs for the JobDistributor |
| not_universal_main.cc | Simple main method for applying a Mover to a set of input Poses |
| not_universal_main.hh | Simple main method for applying a Mover to a set of input Poses |
| standard_mains.cc | |
| standard_mains.hh | Main methods that implement the typical running patterns for executables |
| ► jumping | |
| DisulfPairingLibrary.cc | |
| DisulfPairingLibrary.hh | |
| DisulfPairingsList.cc | |
| DisulfPairingsList.fwd.hh | Fwd headers for ns jumping |
| DisulfPairingsList.hh | |
| JumpSample.cc | |
| JumpSample.hh | |
| JumpSetup.cc | |
| JumpSetup.fwd.hh | |
| JumpSetup.hh | |
| MembraneJump.cc | |
| MembraneJump.fwd.hh | |
| MembraneJump.hh | |
| PairingLibrary.cc | |
| PairingLibrary.fwd.hh | Fwd headers for ns jumping |
| PairingLibrary.hh | |
| RandomSheetBuilder.cc | Secondary structure will hold statistics about secondary structure predictions sources can be from |
| RandomSheetBuilder.hh | |
| ResiduePairJump.cc | Class to create jump transform from a pair of residues |
| ResiduePairJump.fwd.hh | |
| ResiduePairJump.hh | Class to create jump transform from a pair of residues |
| ResiduePairJumpSetup.cc | |
| ResiduePairJumpSetup.fwd.hh | |
| ResiduePairJumpSetup.hh | |
| SameStrand.cc | Secondary structure will hold statistics about secondary structure predictions sources can be from |
| SameStrand.fwd.hh | Fwd headers for ns jumping |
| SameStrand.hh | Secondary structure will hold statistics about secondary structure predictions sources can be from |
| SheetBuilder.cc | Secondary structure will hold statistics about secondary structure predictions sources can be from |
| SheetBuilder.hh | |
| util.cc | |
| util.hh | |
| ► kinematic_closure | |
| ► perturbers | |
| BondAnglePerturber.cc | |
| BondAnglePerturber.fwd.hh | |
| BondAnglePerturber.hh | |
| IdealizeNonPhiPsi.cc | |
| IdealizeNonPhiPsi.fwd.hh | |
| IdealizeNonPhiPsi.hh | |
| Perturber.cc | |
| Perturber.fwd.hh | |
| Perturber.hh | |
| PerturberSet.cc | |
| PerturberSet.fwd.hh | |
| PerturberSet.hh | |
| RamaPerturber.cc | |
| RamaPerturber.fwd.hh | |
| RamaPerturber.hh | |
| readme.hh | |
| UniformPerturber.cc | |
| UniformPerturber.fwd.hh | |
| UniformPerturber.hh | |
| VicinityPerturber.cc | |
| VicinityPerturber.fwd.hh | |
| VicinityPerturber.hh | |
| WalkingBondAnglePerturber.cc | |
| WalkingBondAnglePerturber.fwd.hh | |
| WalkingBondAnglePerturber.hh | |
| WalkingPerturber.cc | |
| WalkingPerturber.fwd.hh | |
| WalkingPerturber.hh | |
| ► pivot_pickers | |
| EndToEndPivots.cc | |
| EndToEndPivots.fwd.hh | |
| EndToEndPivots.hh | |
| FixedOffsetPivots.cc | |
| FixedOffsetPivots.fwd.hh | |
| FixedOffsetPivots.hh | |
| FixedPivots.cc | |
| FixedPivots.fwd.hh | |
| FixedPivots.hh | |
| LoopPivots.cc | |
| LoopPivots.fwd.hh | |
| LoopPivots.hh | |
| PivotPicker.fwd.hh | |
| PivotPicker.hh | |
| readme.hh | |
| StandardPivots.cc | |
| StandardPivots.fwd.hh | |
| StandardPivots.hh | |
| ► solution_pickers | |
| FilteredSolutions.cc | |
| FilteredSolutions.fwd.hh | |
| FilteredSolutions.hh | |
| NearbyFilteredSolutions.fwd.hh | |
| RandomSolutions.cc | |
| RandomSolutions.fwd.hh | |
| RandomSolutions.hh | |
| readme.hh | |
| SolutionPicker.fwd.hh | |
| SolutionPicker.hh | |
| BalancedKicMover.cc | |
| BalancedKicMover.fwd.hh | |
| BalancedKicMover.hh | |
| ClosureProblem.cc | Source file for ClosureProblem |
| ClosureProblem.fwd.hh | Forward header for ClosureProblem |
| ClosureProblem.hh | Header file for ClosureProblem |
| ClosureSolution.cc | Source file for ClosureSolution |
| ClosureSolution.fwd.hh | Forward header for ClosureSolution |
| ClosureSolution.hh | Header file for ClosureSolution |
| internal.cc | Source file for internal helpers |
| internal.hh | |
| KicMover.cc | |
| KicMover.fwd.hh | |
| KicMover.hh | |
| readme.hh | |
| types.hh | Header file for shared types |
| ► kinmatch | |
| FunGroupTK.cc | |
| FunGroupTK.hh | ToolKit for rapid IK based functional group placement |
| ► ligand_docking | |
| ► ligand_options | |
| Interface.cc | |
| Interface.fwd.hh | |
| Interface.hh | |
| interface_distance_functions.cc | |
| interface_distance_functions.hh | |
| ► rdf | |
| RDFBase.fwd.hh | Forward headers for RDFBase |
| RDFBase.hh | A base class that defines an RDF function. These functions computes one or more RDF values for a pair of atoms |
| RDFFunctionCreator.fwd.hh | Forward Header for base class for RDFFunctionCreator |
| RDFFunctionCreator.hh | |
| RDFFunctionFactory.cc | Factory for creating RDFBase objects |
| RDFFunctionFactory.fwd.hh | Forward headers for RDFFunctionFactory |
| RDFFunctionFactory.hh | Headers for RDFFunctionFactory |
| StandardRDFFunctions.cc | |
| StandardRDFFunctions.fwd.hh | Forward headers for standard RDF Functions used by RosettaHTS |
| StandardRDFFunctions.hh | Headers for standard RDF Functions used by RosettaHTS |
| AddHydrogen.cc | Lemmon |
| AddHydrogen.fwd.hh | |
| AddHydrogen.hh | |
| AddHydrogens.cc | Lemmon |
| AddHydrogens.fwd.hh | |
| AddHydrogens.hh | |
| AddHydrogensCreator.hh | This class will create instances of Mover AddHydrogens for the MoverFactory |
| AtomCountFilter.cc | Find packing defects at an interface using packstat score terms |
| AtomCountFilter.hh | Find packing defects at an interface using packstat score terms |
| AtomCountFilterCreator.hh | FilterCreator for the AtomCountFilter |
| ChainExistsFilter.cc | Find packing defects at an interface using packstat score terms |
| ChainExistsFilter.hh | Find packing defects at an interface using packstat score terms |
| ChainExistsFilterCreator.hh | FilterCreator for the ChainExistsFilter |
| CompleteConnectionsFilter.cc | |
| CompleteConnectionsFilter.hh | |
| CompleteConnectionsFilterCreator.hh | FilterCreator for the CompleteConnectionsFilter |
| CompoundTranslate.cc | |
| CompoundTranslate.hh | |
| CompoundTranslateCreator.hh | This class will create instances of Mover CompoundTranslateCreator for the MoverFactory |
| ComputeLigandRDF.cc | A mover for computing RDF functions |
| ComputeLigandRDF.fwd.hh | |
| ComputeLigandRDF.hh | Header file for ComputeLigandRDF mover |
| ComputeLigandRDFCreator.hh | |
| DistributionMap.cc | |
| DistributionMap.hh | |
| FinalMinimizer.cc | |
| FinalMinimizer.fwd.hh | |
| FinalMinimizer.hh | |
| FinalMinimizerCreator.hh | This class will create instances of Mover FinalMinimizerCreator for the MoverFactory |
| grid_functions.cc | |
| grid_functions.hh | |
| GrowLigand.cc | Lemmon |
| GrowLigand.fwd.hh | |
| GrowLigand.hh | |
| GrowLigandCreator.hh | This class will create instances of Mover GrowLigand for the MoverFactory |
| HBondAcceptorFilter.cc | Find packing defects at an interface using packstat score terms |
| HBondAcceptorFilter.hh | Find packing defects at an interface using packstat score terms |
| HBondAcceptorFilterCreator.hh | FilterCreator for the HBondAcceptorFilter |
| HBondDonorFilter.cc | Find packing defects at an interface using packstat score terms |
| HBondDonorFilter.hh | Find packing defects at an interface using packstat score terms |
| HBondDonorFilterCreator.hh | FilterCreator for the HBondDonorFilter |
| HeavyAtomFilter.cc | Find packing defects at an interface using packstat score terms |
| HeavyAtomFilter.hh | Find packing defects at an interface using packstat score terms |
| HeavyAtomFilterCreator.hh | FilterCreator for the HeavyAtomFilter |
| HighResDocker.cc | |
| HighResDocker.fwd.hh | |
| HighResDocker.hh | |
| HighResDockerCreator.hh | This class will create instances of Mover HighResDockerCreator for the MoverFactory |
| InterfaceBuilder.cc | |
| InterfaceBuilder.fwd.hh | |
| InterfaceBuilder.hh | |
| InterfaceScoreCalculator.cc | |
| InterfaceScoreCalculator.fwd.hh | |
| InterfaceScoreCalculator.hh | |
| InterfaceScoreCalculatorCreator.hh | This class will create instances of Mover InterfaceScoreCalculator for the MoverFactory |
| ligand_dock_impl.cc | |
| ligand_dock_impl.hh | |
| ligand_functions.cc | |
| ligand_functions.hh | |
| ligand_scores.cc | |
| ligand_scores.hh | |
| LigandArea.cc | |
| LigandArea.fwd.hh | |
| LigandArea.hh | |
| LigandBaseProtocol.cc | |
| LigandBaseProtocol.hh | |
| LigandDesign.cc | Lemmon |
| LigandDesign.fwd.hh | |
| LigandDesign.hh | |
| LigandDesignCreator.hh | This class will create instances of Mover LigandDesign for the MoverFactory |
| LigandDockingLoaderCreators.hh | Creator classes for the ligand docking DataLoader classes: InterfaceBuilderLoader and MoveMapBuilderLoader |
| LigandDockingLoaders.cc | Implementation of the InterfaceBuilderLoader and MoveMapBuilderLoader classes |
| LigandDockingLoaders.hh | |
| LigandDockProtocol.cc | |
| LigandDockProtocol.fwd.hh | |
| LigandDockProtocol.hh | |
| MinimizeBackbone.cc | |
| MinimizeBackbone.fwd.hh | |
| MinimizeBackbone.hh | |
| MinimizeBackboneCreator.hh | This class will create instances of Mover MinimizeBackboneCreator for the MoverFactory |
| MinimizeLigand.cc | |
| MinimizeLigand.fwd.hh | |
| MinimizeLigand.hh | |
| MolarMassFilter.cc | Find packing defects at an interface using packstat score terms |
| MolarMassFilter.hh | Find packing defects at an interface using packstat score terms |
| MolarMassFilterCreator.hh | FilterCreator for the MolarMassFilter |
| MolecularMassFilter.cc | Find packing defects at an interface using packstat score terms |
| MolecularMassFilter.hh | Find packing defects at an interface using packstat score terms |
| MolecularMassFilterCreator.hh | FilterCreator for the MolecularMassFilter |
| MoveMapBuilder.cc | |
| MoveMapBuilder.fwd.hh | |
| MoveMapBuilder.hh | |
| RandomConformerMover.cc | |
| RandomConformerMover.fwd.hh | |
| RandomConformerMover.hh | |
| RandomConformers.cc | |
| RandomConformers.hh | |
| RandomConformersCreator.hh | This class will create instances of Mover RandomConformersCreator for the MoverFactory |
| ResidueTorsionRestraints.cc | |
| ResidueTorsionRestraints.fwd.hh | |
| ResidueTorsionRestraints.hh | |
| RigidSearchMover.cc | |
| RigidSearchMover.fwd.hh | |
| RigidSearchMover.hh | |
| Rotate.cc | |
| Rotate.fwd.hh | |
| Rotate.hh | |
| RotateCreator.hh | This class will create instances of Mover Rotate for the MoverFactory |
| Rotates.cc | |
| Rotates.fwd.hh | |
| Rotates.hh | |
| RotatesCreator.hh | This class will create instances of Mover Rotates for the MoverFactory |
| ScreeningDocker.cc | |
| ScreeningDocker.fwd.hh | |
| ScreeningDocker.hh | |
| ScreeningDockerCreator.hh | |
| SlideTogether.cc | |
| SlideTogether.hh | |
| SlideTogetherCreator.hh | This class will create instances of Mover SlideTogether for the MoverFactory |
| StartFrom.cc | |
| StartFrom.fwd.hh | |
| StartFrom.hh | Header of classes for resfile options |
| StartFromCreator.hh | This class will create instances of Mover StartFrom for the MoverFactory |
| TetherLigand.cc | |
| TetherLigand.fwd.hh | |
| TetherLigand.hh | |
| Transform.cc | |
| Transform.fwd.hh | |
| Transform.hh | |
| TransformCreator.hh | This class will create instances of Mover Transform for the MoverFactory |
| Translate.cc | |
| Translate.fwd.hh | |
| Translate.hh | |
| TranslateCreator.hh | This class will create instances of Mover Translate for the MoverFactory |
| UnconstrainedTorsionsMover.cc | |
| UnconstrainedTorsionsMover.fwd.hh | |
| UnconstrainedTorsionsMover.hh | |
| WriteLigandMolFile.cc | Ligand MolFile writer |
| WriteLigandMolFile.fwd.hh | Forward header class for Ligand MolFile writer |
| WriteLigandMolFile.hh | Header class for Ligand MolFile writer |
| WriteLigandMolFileCreator.hh | This class will create instances of Mover WriteLigandMolFile for the MoverFactory |
| ► loop_build | |
| LoopBuild.cc | |
| LoopBuild.hh | |
| LoopBuildMover.cc | |
| LoopBuildMover.fwd.hh | |
| LoopBuildMover.hh | |
| LoopMover_SlidingWindow.cc | Kinematic loop closure main protocols |
| LoopMover_SlidingWindow.hh | |
| LoopMover_SlidingWindowCreator.cc | |
| LoopMover_SlidingWindowCreator.hh | Header for LoopMover_SlidingWindowCreator |
| ► loop_modeling | |
| ► loggers | |
| Logger.cc | |
| Logger.fwd.hh | |
| Logger.hh | |
| PdbLogger.cc | |
| PdbLogger.fwd.hh | |
| PdbLogger.hh | |
| ProgressBar.cc | |
| ProgressBar.fwd.hh | |
| ProgressBar.hh | |
| readme.hh | |
| ScoreVsRmsd.cc | |
| ScoreVsRmsd.fwd.hh | |
| ScoreVsRmsd.hh | |
| ► openers | |
| BondAngleOpener.cc | |
| BondAngleOpener.fwd.hh | |
| BondAngleOpener.hh | |
| IdealGeometryOpener.cc | |
| IdealGeometryOpener.fwd.hh | |
| IdealGeometryOpener.hh | |
| LoopOpener.fwd.hh | |
| LoopOpener.hh | |
| NullOpener.fwd.hh | |
| NullOpener.hh | |
| OpenerCollection.cc | |
| OpenerCollection.fwd.hh | |
| OpenerCollection.hh | |
| RamachandranOpener.cc | |
| RamachandranOpener.fwd.hh | |
| RamachandranOpener.hh | |
| readme.hh | |
| types.hh | |
| ► refiners | |
| LocalMinimizationRefiner.cc | |
| LocalMinimizationRefiner.fwd.hh | |
| LocalMinimizationRefiner.hh | |
| readme.hh | |
| RepackingRefiner.cc | |
| RepackingRefiner.fwd.hh | |
| RepackingRefiner.hh | |
| RotamerTrialsRefiner.cc | |
| RotamerTrialsRefiner.fwd.hh | |
| RotamerTrialsRefiner.hh | |
| ► samplers | |
| LegacyKicSampler.cc | |
| LegacyKicSampler.fwd.hh | |
| LegacyKicSampler.hh | |
| readme.hh | |
| ► utilities | |
| AcceptanceCheck.cc | |
| AcceptanceCheck.fwd.hh | |
| AcceptanceCheck.hh | |
| LoopFilter.cc | |
| LoopFilter.fwd.hh | |
| LoopFilter.hh | |
| LoopMoverGroup.cc | |
| LoopMoverGroup.fwd.hh | |
| LoopMoverGroup.hh | |
| PeriodicMover.cc | |
| PeriodicMover.fwd.hh | |
| PeriodicMover.hh | |
| readme.hh | |
| RepeatedMover.cc | |
| RepeatedMover.fwd.hh | |
| RepeatedMover.hh | |
| LoopBuilder.cc | |
| LoopBuilder.fwd.hh | |
| LoopBuilder.hh | |
| LoopMover.cc | |
| LoopMover.fwd.hh | |
| LoopMover.hh | |
| LoopProtocol.cc | |
| LoopProtocol.fwd.hh | |
| LoopProtocol.hh | |
| readme.hh | |
| types.hh | |
| ► loophash | |
| BackboneDB.cc | |
| BackboneDB.hh | I little in the spirit of fragments but way more memory and speed efficient. Backbones are stored as 16bit fixed comma integers. :) |
| Exceptions.hh | |
| FastGapMover.cc | |
| FastGapMover.fwd.hh | Closes gaps |
| FastGapMover.hh | Protocols for closing gaps |
| LocalInserter.cc | |
| LocalInserter.fwd.hh | LocalInserter class forward declarations header |
| LocalInserter.hh | |
| LoopHashDiversifier.cc | |
| LoopHashDiversifier.hh | |
| LoopHashDiversifierCreator.hh | Declaration of the MoverCreator class for the LoopHashDiversifierCreator |
| LoopHashLibrary.cc | |
| LoopHashLibrary.fwd.hh | LoopHashLibrary class forward declarations header |
| LoopHashLibrary.hh | |
| LoopHashLibraryLoader.cc | Load the Loop Hash library using the resource manager |
| LoopHashLibraryLoader.fwd.hh | Load the Loop Hash library using the resource manager |
| LoopHashLibraryLoader.hh | Load the Loop Hash library using the resource manager |
| LoopHashLibraryLoaderCreator.hh | Load the Loop Hash library using the resource manager |
| LoopHashLibraryOptions.cc | Load the Loop Hash library using the resource manager |
| LoopHashLibraryOptions.fwd.hh | Load the Loop Hash library using the resource manager |
| LoopHashLibraryOptions.hh | Load the Loop Hash library using the resource manager |
| LoopHashLibraryOptionsCreator.hh | Load the Loop Hash library using the resource manager |
| LoopHashMap.cc | |
| LoopHashMap.hh | |
| LoopHashMoverWrapper.cc | |
| LoopHashMoverWrapper.hh | |
| LoopHashMoverWrapperCreator.hh | Declaration of the MoverCreator class for the LoopHashMoverWrapper |
| LoopHashRelaxProtocol.cc | |
| LoopHashRelaxProtocol.hh | |
| LoopHashSampler.cc | |
| LoopHashSampler.fwd.hh | LoopHashSampler class forward declarations header |
| LoopHashSampler.hh | |
| Mover_LoopHashRefine.cc | |
| Mover_LoopHashRefine.hh | |
| MPI_LoopHashRefine.cc | |
| MPI_LoopHashRefine.hh | |
| MPI_LoopHashRefine_Emperor.cc | |
| MPI_LoopHashRefine_Emperor.hh | |
| MPI_LoopHashRefine_Master.cc | |
| MPI_LoopHashRefine_Master.hh | |
| WorkUnit_LoopHash.cc | |
| WorkUnit_LoopHash.hh | |
| ► loops | |
| ► loop_closure | |
| ► ccd | |
| ccd_closure.cc | |
| ccd_closure.hh | |
| CcdLoopClosureMover.cc | |
| CcdLoopClosureMover.fwd.hh | Fwd headers for ns loops |
| CcdLoopClosureMover.hh | Header file for CcdLoopClosureMover protocol |
| FASelectSlidingWindowLoopClosure.cc | |
| FASelectSlidingWindowLoopClosure.fwd.hh | Fwd headers for FASelectSlidingWindowLoopClosure |
| FASelectSlidingWindowLoopClosure.hh | |
| LoopClosure.cc | |
| LoopClosure.fwd.hh | Fwd headers for ns loops |
| LoopClosure.hh | |
| ShortLoopClosure.cc | |
| ShortLoopClosure.fwd.hh | |
| ShortLoopClosure.hh | |
| SlidingWindowLoopClosure.cc | |
| SlidingWindowLoopClosure.fwd.hh | Fwd headers for ns loops |
| SlidingWindowLoopClosure.hh | Header file for SlidingWindowLoopClosure protocol |
| WidthFirstSlidingWindowLoopClosure.cc | |
| WidthFirstSlidingWindowLoopClosure.fwd.hh | Fwd headers for ns loops |
| WidthFirstSlidingWindowLoopClosure.hh | |
| ► kinematic_closure | |
| KinematicMover.cc | |
| KinematicMover.fwd.hh | KinematicMover forward declarations header |
| KinematicMover.hh | |
| KinematicPerturber.cc | Implementations for KinematicPerturbers used by the kinematic mover |
| KinematicPerturber.fwd.hh | KinematicPerturber forward declarations header |
| KinematicPerturber.hh | Header file for KinematicPerturbers used by the kineamtic mover |
| KinematicWrapper.cc | KinematicWrapper methods implemented - this is a mover which simplifies use of KinematicMover loop modeling |
| KinematicWrapper.fwd.hh | KinematicWrapper forward declarations header |
| KinematicWrapper.hh | Wrapper for KinematicMover - useful when only apply() is available |
| ► loop_mover | |
| ► perturb | |
| LoopMover_CCD.cc | |
| LoopMover_CCD.fwd.hh | LoopMover_Perutrb_CCD forward declaration |
| LoopMover_CCD.hh | |
| LoopMover_CCDCreator.hh | Header for LoopMover_CCDCreator |
| LoopMover_KIC.cc | |
| LoopMover_KIC.fwd.hh | LoopMover_Perturb_KIC forward declaration |
| LoopMover_KIC.hh | |
| LoopMover_KICCreator.hh | |
| LoopMover_QuickCCD.cc | |
| LoopMover_QuickCCD.fwd.hh | LoopMover_QuickCCD forward declaration |
| LoopMover_QuickCCD.hh | |
| LoopMover_QuickCCD_Moves.cc | |
| LoopMover_QuickCCD_Moves.fwd.hh | LoopMover_QuickCCD_Moves forward declaration |
| LoopMover_QuickCCD_Moves.hh | |
| LoopMover_QuickCCD_MovesCreator.hh | |
| LoopMover_QuickCCDCreator.hh | Header for LoopMover_QuickCCDCreator |
| ► refine | |
| LoopMover_Backrub.cc | |
| LoopMover_Backrub.fwd.hh | LoopMover_Backrub forward declaration |
| LoopMover_Backrub.hh | |
| LoopMover_BackrubCreator.hh | Header for LoopMover_BackrubCreator |
| LoopMover_CCD.cc | |
| LoopMover_CCD.fwd.hh | |
| LoopMover_CCD.hh | |
| LoopMover_CCDCreator.hh | |
| LoopMover_KIC.cc | |
| LoopMover_KIC.fwd.hh | LoopMover_Backrub forward declaration |
| LoopMover_KIC.hh | |
| LoopMover_KICCreator.hh | |
| LoopRefineInnerCycle.cc | Abstract class to define interface for all types of "inner cycle" operations used for loop refinement |
| LoopRefineInnerCycle.fwd.hh | Forward declaration |
| LoopRefineInnerCycle.hh | Abstract class to define interface for all types of "inner cycle" operations used for loop refinement |
| LoopRefineInnerCycleContainer.cc | This class is a LoopRefineInnerCycle that contains one or more other LoopRefineInnerCycles to allow a developer to quickly string together existing LoopRefineInnerCycles in new ways to create new loop refinement protocols |
| LoopRefineInnerCycleContainer.fwd.hh | Forward declaration |
| LoopRefineInnerCycleContainer.hh | This class is a LoopRefineInnerCycle that contains one or more other LoopRefineInnerCycles to allow a developer to quickly string together existing LoopRefineInnerCycles in new ways to create new loop refinement protocols |
| LoopRefineInnerCycleContainerCreator.hh | |
| LoopRefineInnerCycleFactory.cc | Factory for creating LoopRefineInnerCycle objects |
| LoopRefineInnerCycleFactory.fwd.hh | |
| LoopRefineInnerCycleFactory.hh | Factory for creating LoopRefineInnerCycle objects |
| RepackTrial.cc | |
| RepackTrial.fwd.hh | Forward declaration |
| RepackTrial.hh | Abstract class to define interface for all types of "inner cycle" operations used for loop refinement |
| RepackTrialCreator.hh | |
| ShearMinCCDTrial.cc | Concrete class derived from LoopRefineInnerCycle to implement the CCD min trial flavor of inner cycle refinement |
| ShearMinCCDTrial.fwd.hh | Forward declaration |
| ShearMinCCDTrial.hh | Concrete class derived from LoopRefineInnerCycle to implement the CCD min trial flavor of inner cycle refinement |
| ShearMinCCDTrialCreator.hh | |
| SmallMinCCDTrial.cc | |
| SmallMinCCDTrial.fwd.hh | Forward declaration |
| SmallMinCCDTrial.hh | Perform a small move followed CCD closure, packing and minimization |
| SmallMinCCDTrialCreator.hh | |
| IndependentLoopMover.cc | Loop mover base class |
| IndependentLoopMover.fwd.hh | |
| IndependentLoopMover.hh | |
| LoopMover.cc | Loop mover base class |
| LoopMover.fwd.hh | LoopMover base classes |
| LoopMover.hh | |
| ► loops_definers | |
| LoopsDatabaseDefiner.cc | A loops definer is creates a serialized loops list |
| LoopsDatabaseDefiner.fwd.hh | LoopsDatabaseDefiner class forward declarations header |
| LoopsDatabaseDefiner.hh | A loops definer is creates a serialized loops list |
| LoopsDatabaseDefinerCreator.cc | LoopsDatabaseDefinerCreator for the LoosDatabaseDefiner load-time factory registration scheme |
| LoopsDatabaseDefinerCreator.fwd.hh | Forward Header for base class for LoopsDatabaseDefinerCreator |
| LoopsDatabaseDefinerCreator.hh | Header for LoopsDatabaseDefinerCreator for the LoosDatabaseDefiner load-time factory registration scheme |
| LoopsDefiner.fwd.hh | LoopsDefiner class forward declarations header |
| LoopsDefiner.hh | A loops definer is creates a serialized loops list |
| LoopsDefinerCreator.fwd.hh | LoopsDefinerCreator class forward declarations header |
| LoopsDefinerCreator.hh | Base class LoopsDefinerCreator for the load-time factory registration scheme |
| LoopsDefinerFactory.cc | Factory for creating LoopsDefiner objects |
| LoopsDefinerFactory.fwd.hh | |
| LoopsDefinerFactory.hh | Factory for creating LoopsDefiner objects |
| LoopsDefinerLoader.cc | Implementation the LoopsDefinerLoader class which implements the DataLoader interface |
| LoopsDefinerLoader.hh | Declartion of the XML loops_definers's LoopsDefinerLoader class |
| LoopsDefinerLoaderCreator.hh | Creator classe for the LoopsDefinerLoader classe |
| LoopsExplicitDefiner.cc | A loops definer is creates a serialized loops list |
| LoopsExplicitDefiner.fwd.hh | LoopsExplicitDefiner class forward declarations header |
| LoopsExplicitDefiner.hh | A loops definer is creates a serialized loops list |
| LoopsExplicitDefinerCreator.cc | LoopsExplicitDefinerCreator for the LoosExplicitDefiner load-time factory registration scheme |
| LoopsExplicitDefinerCreator.fwd.hh | Forward Header for base class for LoopsExplicitDefinerCreator |
| LoopsExplicitDefinerCreator.hh | Header for LoopsExplicitDefinerCreator for the LoosExplicitDefiner load-time factory registration scheme |
| LoopsFileDefiner.cc | A loops definer is creates a serialized loops list |
| LoopsFileDefiner.fwd.hh | LoopsFileDefiner class forward declarations header |
| LoopsFileDefiner.hh | A loops definer is creates a serialized loops list |
| LoopsFileDefinerCreator.cc | LoopsFileDefinerCreator for the LoosFileDefiner load-time factory registration scheme |
| LoopsFileDefinerCreator.fwd.hh | Forward Header for base class for LoopsFileDefinerCreator |
| LoopsFileDefinerCreator.hh | Header for LoopsFileDefinerCreator for the LoosFileDefiner load-time factory registration scheme |
| util.cc | Utility functions useful in LoopDefiner classes |
| util.hh | Utility functions useful in LoopDefiner classes |
| Exceptions.hh | |
| FoldTreeFromLoopsWrapper.cc | |
| FoldTreeFromLoopsWrapper.fwd.hh | |
| FoldTreeFromLoopsWrapper.hh | |
| FoldTreeFromLoopsWrapperCreator.hh | |
| Loop.cc | |
| Loop.fwd.hh | Loop class forward declarations header |
| Loop.hh | |
| loopfinder.cc | |
| loopfinder.hh | |
| LoopMoverFactory.cc | |
| LoopMoverFactory.fwd.hh | Report data to database |
| LoopMoverFactory.hh | Factory for creating LoopMover objects |
| looprelax_protocols.cc | |
| looprelax_protocols.hh | |
| Loops.cc | |
| Loops.fwd.hh | Loops and Loop class forward declarations header |
| Loops.hh | |
| Loops.tmpl.hh | |
| loops_main.cc | Loop building tools |
| loops_main.hh | |
| LoopsFileFallbackConfiguration.cc | |
| LoopsFileFallbackConfiguration.fwd.hh | Forward hearder for OptionsSystemFallback class |
| LoopsFileFallbackConfiguration.hh | |
| LoopsFileFallbackConfigurationCreator.hh | |
| LoopsFileIO.cc | |
| LoopsFileIO.fwd.hh | LoopsFileIO forward declarations header |
| LoopsFileIO.hh | This class exists to handle the reading and writing of loops files |
| LoopsFileLoader.cc | |
| LoopsFileLoader.fwd.hh | |
| LoopsFileLoader.hh | |
| LoopsFileLoaderCreator.hh | |
| LoopsFileOptions.cc | |
| LoopsFileOptions.fwd.hh | LoopsFileOptions forward declarations header |
| LoopsFileOptions.hh | |
| LoopsFileOptionsCreator.hh | |
| make_loops.cc | |
| make_loops.hh | |
| util.cc | |
| util.hh | |
| ► make_rot_lib | |
| MakeRotLib.cc | |
| MakeRotLib.hh | |
| RotData.cc | |
| RotData.hh | |
| ► match | |
| ► downstream | |
| ActiveSiteGrid.cc | |
| ActiveSiteGrid.fwd.hh | |
| ActiveSiteGrid.hh | |
| ClassicMatchAlgorithm.cc | |
| ClassicMatchAlgorithm.fwd.hh | |
| ClassicMatchAlgorithm.hh | |
| DownstreamAlgorithm.cc | |
| DownstreamAlgorithm.fwd.hh | |
| DownstreamAlgorithm.hh | Declaration for the base-class algorithm that creates hits from an upstream builder, while managing the logic of their creation. Furthermore, the downstream algorithm manages update of hits from previous rounds should they loose their potential to result in matches |
| DownstreamBuilder.cc | |
| DownstreamBuilder.fwd.hh | |
| DownstreamBuilder.hh | |
| GeometrySecMatchRPE.cc | |
| GeometrySecMatchRPE.fwd.hh | |
| GeometrySecMatchRPE.hh | |
| LigandConformerBuilder.cc | |
| LigandConformerBuilder.fwd.hh | |
| LigandConformerBuilder.hh | |
| RigidLigandBuilder.cc | |
| RigidLigandBuilder.fwd.hh | |
| RigidLigandBuilder.hh | |
| ScoringSecMatchRPE.cc | |
| ScoringSecMatchRPE.fwd.hh | |
| ScoringSecMatchRPE.hh | |
| SecMatchEvaluatorFactory.cc | |
| SecMatchEvaluatorFactory.hh | |
| SecMatchResiduePairEvaluator.cc | |
| SecMatchResiduePairEvaluator.fwd.hh | |
| SecMatchResiduePairEvaluator.hh | |
| SecondaryMatcherToDownstreamResidue.cc | Class implementation for secondary matcher that generates upstream-only hits matching the geometry of one upstream residue with another upstream residue generated in a previous round |
| SecondaryMatcherToDownstreamResidue.fwd.hh | |
| SecondaryMatcherToDownstreamResidue.hh | Class declaration for secondary matcher that generates upstream-only hits matching the geometry of one upstream residue with another upstream residue generated in a previous round |
| SecondaryMatcherToUpstreamResidue.cc | Class implementation for secondary matcher that generates upstream-only hits matching the geometry of one upstream residue with another upstream residue generated in a previous round |
| SecondaryMatcherToUpstreamResidue.fwd.hh | |
| SecondaryMatcherToUpstreamResidue.hh | Class declaration for secondary matcher that generates upstream-only hits matching the geometry of one upstream residue with another upstream residue generated in a previous round |
| ► output | |
| DownstreamRMSEvaluator.cc | |
| DownstreamRMSEvaluator.fwd.hh | |
| DownstreamRMSEvaluator.hh | |
| LimitHitsPerRotamerFilter.cc | |
| LimitHitsPerRotamerFilter.fwd.hh | |
| LimitHitsPerRotamerFilter.hh | |
| MatchConsolidator.cc | |
| MatchConsolidator.fwd.hh | |
| MatchConsolidator.hh | |
| MatchEvaluator.cc | |
| MatchEvaluator.fwd.hh | Forward declaration for abstract class to filter matches |
| MatchEvaluator.hh | |
| MatchFilter.cc | Implementation for abstract filter class |
| MatchFilter.fwd.hh | Forward declaration for abstract class to filter matches |
| MatchFilter.hh | Declaration for abstract class to filter matches |
| MatchGrouper.cc | |
| MatchGrouper.fwd.hh | |
| MatchGrouper.hh | |
| MatchOutputter.cc | Implementation of class to write output matches that pass filters This class does not "look ahead" to future matches to decide whether the current match to process should be output, however, filters are able to keep a history of what they've output so far |
| MatchOutputter.fwd.hh | Forward declaration for no-lookahead match processor |
| MatchOutputter.hh | |
| MatchProcessor.cc | |
| MatchProcessor.fwd.hh | |
| MatchProcessor.hh | |
| MatchScoreWriter.cc | |
| MatchScoreWriter.fwd.hh | |
| MatchScoreWriter.hh | |
| OutputWriter.cc | Implementation for the class to write output matches that have (presumably) passed the output filters |
| OutputWriter.fwd.hh | Forward declaration of class to write output matches that have (presumably) passed the output filters |
| OutputWriter.hh | |
| PDBWriter.cc | Forward declaration of class to write output matches that have (presumably) passed the output filters |
| PDBWriter.fwd.hh | |
| PDBWriter.hh | |
| PoseInserter.cc | |
| PoseInserter.fwd.hh | |
| PoseInserter.hh | |
| ProcessorFactory.cc | |
| ProcessorFactory.fwd.hh | |
| ProcessorFactory.hh | Implementation for a factory class responsible for instantiating MatchProcessor classes |
| SameChiBinComboGrouper.cc | |
| SameChiBinComboGrouper.fwd.hh | |
| SameChiBinComboGrouper.hh | |
| SameRotamerComboGrouper.cc | |
| SameRotamerComboGrouper.fwd.hh | |
| SameRotamerComboGrouper.hh | |
| SameSequenceGrouper.cc | |
| SameSequenceGrouper.fwd.hh | |
| SameSequenceGrouper.hh | |
| UpstreamCollisionFilter.cc | |
| UpstreamCollisionFilter.fwd.hh | Forward declaration for abstract class to filter matches |
| UpstreamCollisionFilter.hh | Implementation for class to filter matches where the upstream residues collide |
| UpstreamDownstreamCollisionFilter.cc | |
| UpstreamDownstreamCollisionFilter.fwd.hh | Forward declaration for abstract class to filter matches |
| UpstreamDownstreamCollisionFilter.hh | Implementation for class to filter matches where the upstream residues collide |
| UpstreamHitCacher.cc | |
| UpstreamHitCacher.fwd.hh | Forward declaration for class to cache and recall the conformations of upstream hits |
| UpstreamHitCacher.hh | Declaration for class to cache and recall the conformations of upstream hits |
| WriteKinemageOutputter.cc | Forward declaration of class to write output matches that have (presumably) passed the output filters |
| WriteKinemageOutputter.fwd.hh | |
| WriteKinemageOutputter.hh | |
| WriteUpstreamCoordinateKineamge.cc | |
| WriteUpstreamCoordinateKineamge.fwd.hh | |
| WriteUpstreamCoordinateKineamge.hh | |
| ► upstream | |
| OriginalScaffoldBuildPoint.cc | |
| OriginalScaffoldBuildPoint.fwd.hh | |
| OriginalScaffoldBuildPoint.hh | |
| ProteinSCSampler.cc | Class declarations for base class and simple derived class for SC sampling |
| ProteinSCSampler.fwd.hh | Forward declaration for base class and simple derived class for SC sampling in matcher |
| ProteinSCSampler.hh | Class declarations for base class and simple derived class for SC sampling |
| ProteinUpstreamBuilder.cc | |
| ProteinUpstreamBuilder.fwd.hh | |
| ProteinUpstreamBuilder.hh | |
| ScaffoldBuildPoint.cc | |
| ScaffoldBuildPoint.fwd.hh | |
| ScaffoldBuildPoint.hh | |
| UpstreamBuilder.cc | |
| UpstreamBuilder.fwd.hh | |
| UpstreamBuilder.hh | |
| UpstreamResTypeGeometry.cc | |
| UpstreamResTypeGeometry.fwd.hh | Forward declaration for class to measure the geometry of a given ResidueType |
| UpstreamResTypeGeometry.hh | |
| BumpGrid.cc | |
| BumpGrid.fwd.hh | |
| BumpGrid.hh | |
| Hit.cc | Constructors for match_dspos1 |
| Hit.fwd.hh | Hit class forward declaration |
| Hit.hh | Hit typedef |
| Matcher.cc | |
| Matcher.fwd.hh | |
| Matcher.hh | |
| MatcherMover.cc | Implementation of mover wrapper for matcher |
| MatcherMover.fwd.hh | |
| MatcherMover.hh | |
| MatcherMoverCreator.hh | This class will create instances of Mover FlxbbDesign for the MoverFactory |
| MatcherTask.cc | |
| MatcherTask.fwd.hh | |
| MatcherTask.hh | |
| MatchPositionModifiers.cc | Implementations for MatchPositionModifiers |
| MatchPositionModifiers.fwd.hh | Forward declaration for MatchPositionModifiers |
| MatchPositionModifiers.hh | Header file for MatchPositionModifiers |
| MatchSet.cc | |
| MatchSet.fwd.hh | |
| MatchSet.hh | |
| OccupiedSpaceHash.cc | Declaration for classes in 6D hasher |
| OccupiedSpaceHash.fwd.hh | |
| OccupiedSpaceHash.hh | Declaration for classes in 6D hasher |
| VoxelSetIterator.cc | Implementation of the VoxelSetIterator class |
| VoxelSetIterator.fwd.hh | |
| VoxelSetIterator.hh | Forward declaration for iterator to traverse the 64 bins each hit covers |
| ► md | |
| CartesianMD.cc | |
| CartesianMD.fwd.hh | |
| CartesianMD.hh | Cartesian MD |
| CartesianMDCreator.hh | |
| MDBase.cc | Initialization for MD |
| MDBase.fwd.hh | Initialization for MD |
| MDBase.hh | Initialization for MD |
| MDConstants.hh | Protocols/md package type declarations |
| Rattle.hh | Rattle bond length constrainer for CartesianMD |
| thermostat.hh | Thermostat for MD simulation |
| ► medal | |
| MedalExchangeMover.cc | |
| MedalExchangeMover.fwd.hh | |
| MedalExchangeMover.hh | |
| MedalMain.cc | |
| MedalMain.hh | |
| MedalMover.cc | |
| MedalMover.fwd.hh | |
| MedalMover.hh | |
| util.cc | |
| util.hh | |
| ► membrane | |
| CreateMembranePoseMover.cc | Create Membrane Pose - Mover Class |
| CreateMembranePoseMover.fwd.hh | Create Membrane Pose - Mover Class |
| CreateMembranePoseMover.hh | Create Membrane Pose - Mover Class |
| CreateMembranePoseMoverCreator.hh | Create Membrane Pose - Mover Class |
| MembraneUnitTestMover.cc | Top-Level Unit Test for the Membrane Protein Factory (Mover Class) |
| MembraneUnitTestMover.fwd.hh | |
| MembraneUnitTestMover.hh | Top-Level Unit Test for the Membrane Protein Factory (Mover Class) |
| ► metal_interface | |
| AddZincSiteConstraints.cc | Adds metal binding site geometry constraints to pose |
| AddZincSiteConstraints.fwd.hh | AddZincSiteConstraints protocol-mover forward declarations header |
| AddZincSiteConstraints.hh | Adds metal binding site geometry constraints to pose |
| FindClosestAtom.cc | |
| FindClosestAtom.hh | Finds the closest atom in a given residue to a point (usually a zinc atom) |
| MatchGrafter.cc | Takes a scaffold protein and a match pdb from RosettaMatch, grafts the match onto the protein. For zinc homodimer design, it can then combine two grafted poses by overlaying the zinc atoms |
| MatchGrafter.fwd.hh | MatchGrafter protocol-mover forward declarations header |
| MatchGrafter.hh | Takes a scaffold protein and a match pdb from RosettaMatch, grafts the match onto the protein. For zinc homodimer design, it can then combine two grafted poses by overlaying the zinc atoms |
| MetalSiteResidue.cc | Stores data that describes a metal-coordinating residue |
| MetalSiteResidue.fwd.hh | MetalSiteResidue protocol-mover forward declarations header |
| MetalSiteResidue.hh | Stores data that describes a metal-coordinating residue |
| ZincHeterodimerMover.cc | ZincHeterodimerMover methods implemented - see apps/pilot/rjha/README for details |
| ZincHeterodimerMover.fwd.hh | ZincHeterodimerMover protocol-mover forward declarations header |
| ZincHeterodimerMover.hh | ZincHeterodimerMover protocol main mover |
| ZincSiteFinder.cc | |
| ZincSiteFinder.fwd.hh | ZincSiteFinder protocol-mover forward declarations header |
| ZincSiteFinder.hh | |
| ► motif_grafting | |
| ► movers | |
| MotifGraftCreator.hh | |
| MotifGraftMover.cc | |
| MotifGraftMover.hh | |
| ► motif_hash | |
| motif_hash_stuff.cc | |
| motif_hash_stuff.fwd.hh | |
| motif_hash_stuff.hh | |
| ► motifs | |
| BuildPosition.cc | Position where motifs are built in MotifSearch |
| BuildPosition.fwd.hh | Forward declaration for position where motifs are built in MotifSearch |
| BuildPosition.hh | Class declaration for position where motifs are built in MotifSearch |
| IRCollection.cc | Implmentation of interaction motifs |
| IRCollection.fwd.hh | Forward declaration for sets of interaction motifis between residues |
| IRCollection.hh | Class declaration for collections of inverse rotamers |
| LigandMotifSearch.cc | Ligand motif searching protocol |
| LigandMotifSearch.fwd.hh | Forward declaration for interaction motif search protocol |
| LigandMotifSearch.hh | Class declaration for ligand motif searching protocol |
| Motif.cc | Implementation of interaction motifs |
| Motif.fwd.hh | Forward declaration for interaction motif between residues |
| Motif.hh | Header for interaction motif between residues |
| motif_utils.cc | Motif helper/conversion/io functions |
| motif_utils.hh | Header for motif helper/conversion/io functions |
| MotifDnaPacker.cc | |
| MotifDnaPacker.fwd.hh | |
| MotifDnaPacker.hh | |
| MotifDnaPackerCreator.hh | This class will create instances of Mover MotifDnaPacker for the MoverFactory |
| MotifHit.cc | Class that holds information about a motif in the context of the search |
| MotifHit.fwd.hh | Forward declaration for class that holds information about a motif in the context of the search |
| MotifHit.hh | Class declaration for class that holds information about a motif in the context of the search |
| MotifLibrary.cc | Implementation of interaction motifs |
| MotifLibrary.fwd.hh | Forward declaration for sets of interaction motifis between residues |
| MotifLibrary.hh | Class declaration for sets of interaction motifs between residues |
| MotifSearch.cc | Motif searching protocol |
| MotifSearch.fwd.hh | Forward declaration for interaction motif search protocol |
| MotifSearch.hh | Class declaration for motif searching protocol |
| SingleMotif.cc | |
| SingleMotif.fwd.hh | Forward declaration for interaction motif between residues |
| SingleMotif.hh | Header for interaction motif between residues |
| useful_code.cc | |
| ► moves | |
| ► mc_convergence_checks | |
| ConvergenceCheck.fwd.hh | |
| ConvergenceCheck.hh | |
| BoolMover.cc | |
| BoolMover.hh | |
| CanonicalSamplingMover.cc | |
| CanonicalSamplingMover.fwd.hh | |
| CanonicalSamplingMover.hh | |
| ChangeFoldTreeMover.fwd.hh | |
| ChangeFoldTreeMover.hh | ChangeFoldTreeMover |
| CompositionMover.cc | |
| CompositionMover.fwd.hh | |
| CompositionMover.hh | |
| CyclicMover.cc | |
| CyclicMover.fwd.hh | |
| CyclicMover.hh | |
| DsspMover.cc | Performs dssp and set secondary structure to pose |
| DsspMover.fwd.hh | |
| DsspMover.hh | Header file of DsspMover.cc |
| DsspMoverCreator.hh | |
| DualMonteCarlo.cc | |
| DualMonteCarlo.fwd.hh | "dual" MonteCarlo header - wraps MonteCarlo to allow for centroid MonteCarlo scoring of a fullatom pose (or other similar situations) |
| DualMonteCarlo.hh | "dual" MonteCarlo wraps MonteCarlo to allow for centroid MonteCarlo scoring of a fullatom pose (or other similar situations) |
| FilterMover.cc | |
| FilterMover.fwd.hh | |
| FilterMover.hh | |
| IfMover.cc | |
| IfMover.hh | |
| IfMoverCreator.hh | |
| IteratedConvergenceMover.cc | Implementation of IteratedConvergenceMover, class to repeatedly apply a submover until filter convergence is reached |
| IteratedConvergenceMover.fwd.hh | Forward declaration of the mover class to repeatedly apply a submover until filter convergence is reached |
| IteratedConvergenceMover.hh | Mover class to repeatedly apply a submover until filter convergence is reached |
| IteratedConvergenceMoverCreator.hh | This class will create instances of Mover IteratedConvergenceMover for the MoverFactory |
| JumpOutMover.cc | |
| JumpOutMover.fwd.hh | |
| JumpOutMover.hh | JumpOutMover |
| MonteCarlo.cc | |
| MonteCarlo.fwd.hh | |
| MonteCarlo.hh | |
| MonteCarlo.tmpl.hh | Implentation for MonteCarlo template functions |
| MonteCarloExceptionConverge.fwd.hh | |
| MonteCarloExceptionConverge.hh | |
| MonteCarloStatus.cc | |
| MonteCarloStatus.hh | |
| Mover.cc | Method code and full headers for Mover– keeps heavily-included Mover.hh small and concise to maximize compiling efficiency and to make the class definitions easier to read |
| Mover.fwd.hh | |
| Mover.hh | : A mover is an object that can apply a conformational change to a pose |
| MoverContainer.cc | Apply functions for classes of type MoverContainer |
| MoverContainer.fwd.hh | MoverContainer forward declarations header |
| MoverContainer.hh | Base class for containers of movers such as SequenceMover |
| MoverContainerCreator.hh | |
| MoverCreator.cc | |
| MoverCreator.hh | Base class for MoverCreators for the Mover load-time factory registration scheme |
| MoverFactory.cc | |
| MoverFactory.fwd.hh | |
| MoverFactory.hh | |
| MoverForPoseList.cc | |
| MoverForPoseList.fwd.hh | |
| MoverForPoseList.hh | : In addition to applying to a pose, this mover can apply to a vector1 of poses |
| MoverStatistics.cc | Keeps track of the acceptance_rate of a Mover |
| MoverStatistics.hh | Keeps track of the acceptance_rate of a Mover |
| MoverStatus.cc | |
| MoverStatus.hh | Return status enum for Movers |
| NullMover.cc | |
| NullMover.fwd.hh | |
| NullMover.hh | |
| OutputMovers.cc | File to contain classes that deal with output and pdb dumping |
| OutputMovers.fwd.hh | OutputMovers forward declarations header |
| OutputMovers.hh | File to contain classes that deal with output and pdb dumping |
| PyMolMover.cc | Send infromation to PyMol |
| PyMolMover.fwd.hh | |
| PyMolMover.hh | Send infromation to PyMol |
| PyMolMoverCreator.hh | |
| RampingMover.cc | Mover class for ramping the repulsive term of a score function over the course of several apply() evaluations |
| RampingMover.fwd.hh | |
| RampingMover.hh | |
| RampingMoverCreator.hh | This class will create instances of Mover RampingMover for the MoverFactory |
| RepeatMover.cc | Method definitions for RepeatMover |
| RepeatMover.fwd.hh | |
| RepeatMover.hh | Declarations and simple accessor/mutator definitions for RepeatMover |
| ReplicaExchangeMC.cc | Implementing a Recplica Exchange Monte Carlo Mover |
| ReplicaExchangeMC.fwd.hh | Implementing a Recplica Exchange Monte Carlo Mover |
| ReplicaExchangeMC.hh | Implementing a Recplica Exchange Monte Carlo Mover |
| ResId.cc | |
| ResId.fwd.hh | |
| ResId.hh | A simple base class providing common access to a residue identity for movers and filters. The anticipated usage is to derive movers and filters multiply, from the relevant base class and from ResId and make these movers/filters use the residue id encapsulated in this class |
| SimulatedTempering.cc | |
| SimulatedTempering.fwd.hh | |
| SimulatedTempering.hh | |
| StructureRestrictor.cc | Lookup relevant chains for a structure in a table |
| StructureRestrictor.fwd.hh | Lookup relevant chains for a structure in a table |
| StructureRestrictor.hh | Lookup relevant chains for a structure in a table |
| TemperatuerController.fwd.hh | |
| TrialCounter.cc | |
| TrialCounter.fwd.hh | |
| TrialCounter.hh | |
| TrialMover.cc | |
| TrialMover.fwd.hh | TrialMover forward declarations header |
| TrialMover.hh | |
| util.cc | |
| util.hh | |
| WhileMover.cc | |
| WhileMover.fwd.hh | |
| WhileMover.hh | |
| ► multistate_design | |
| MetricCalculatorFitnessFunction.cc | |
| MetricCalculatorFitnessFunction.fwd.hh | |
| MetricCalculatorFitnessFunction.hh | |
| MultiStateAggregateFunction.cc | |
| MultiStateAggregateFunction.fwd.hh | |
| MultiStateAggregateFunction.hh | |
| MultiStateEntity.cc | |
| MultiStateEntity.fwd.hh | |
| MultiStateEntity.hh | |
| MultiStateFitnessFunction.cc | |
| MultiStateFitnessFunction.fwd.hh | |
| MultiStateFitnessFunction.hh | |
| MultiStatePacker.cc | |
| MultiStatePacker.fwd.hh | |
| MultiStatePacker.hh | |
| PackingState.cc | |
| PackingState.fwd.hh | |
| PackingState.hh | For multistate design that is based on (re)use of packer information (RotamerSets and InteractionGraph) |
| PartitionAggregateFunction.cc | |
| PartitionAggregateFunction.fwd.hh | |
| PartitionAggregateFunction.hh | |
| SingleState.cc | |
| SingleState.fwd.hh | |
| SingleState.hh | |
| SingleStateEntityData.cc | |
| SingleStateEntityData.fwd.hh | |
| SingleStateEntityData.hh | |
| SingleStateFitnessFunction.cc | |
| SingleStateFitnessFunction.fwd.hh | |
| SingleStateFitnessFunction.hh | |
| util.cc | Collection of useful utilities for setting up and using a GeneticAlgorithm with multistate design |
| util.hh | |
| ► ncbb | |
| ► oop | |
| OopCreatorMover.cc | |
| OopCreatorMover.fwd.hh | |
| OopCreatorMover.hh | |
| OopCreatorMoverCreator.fwd.hh | |
| OopCreatorMoverCreator.hh | |
| OopDockDesignProtocol.cc | |
| OopDockDesignProtocol.fwd.hh | |
| OopDockDesignProtocol.hh | |
| OopDockDesignProtocolCreator.fwd.hh | |
| OopDockDesignProtocolCreator.hh | |
| NcbbDockDesignProtocol.cc | |
| NcbbDockDesignProtocol.fwd.hh | |
| NcbbDockDesignProtocol.hh | |
| NcbbDockDesignProtocolCreator.fwd.hh | |
| NcbbDockDesignProtocolCreator.hh | |
| ► neighbor | |
| Neighborhood.cc | |
| Neighborhood.hh | |
| ► noesy_assign | |
| Assignment.cc | |
| Assignment.fwd.hh | |
| Assignment.hh | |
| CovalentCompliance.cc | |
| CovalentCompliance.hh | |
| CrossPeak.cc | |
| CrossPeak.fwd.hh | |
| CrossPeak.hh | |
| CrossPeakInfo.cc | |
| CrossPeakInfo.fwd.hh | |
| CrossPeakInfo.hh | |
| CrossPeakList.cc | |
| CrossPeakList.fwd.hh | |
| CrossPeakList.hh | |
| CrossPeakList.impl.hh | |
| CyanaModule.cc | |
| CyanaModule.hh | |
| DistanceScoreMover.cc | |
| DistanceScoreMover.fwd.hh | |
| DistanceScoreMover.hh | |
| Exceptions.hh | |
| FloatingResonance.cc | |
| FloatingResonance.fwd.hh | |
| FloatingResonance.hh | |
| FoldResonance.fwd.hh | |
| FoldResonance.hh | |
| FragsToAtomDist.cc | |
| FragsToAtomDist.fwd.hh | |
| FragsToAtomDist.hh | |
| MethylNames.cc | |
| MethylNames.hh | |
| NoesyModule.cc | Main hook-up for the automatic NOESY assignment module |
| NoesyModule.fwd.hh | |
| NoesyModule.hh | Main hook-up for the automatic NOESY assignment module |
| NoesyModule.impl.hh | |
| PeakAssignment.cc | |
| PeakAssignment.fwd.hh | |
| PeakAssignment.hh | |
| PeakAssignmentOptionKeys.hh | |
| PeakAssignmentParameters.cc | |
| PeakAssignmentParameters.hh | |
| PeakAssignmentResidueMap.cc | |
| PeakAssignmentResidueMap.fwd.hh | |
| PeakAssignmentResidueMap.hh | |
| PeakCalibrator.cc | |
| PeakCalibrator.fwd.hh | |
| PeakCalibrator.hh | |
| PeakFileFormat.cc | |
| PeakFileFormat.fwd.hh | |
| PeakFileFormat.hh | |
| PeakFileFormat_Sparky.cc | |
| PeakFileFormat_Sparky.hh | |
| PeakFileFormat_xpk.cc | |
| PeakFileFormat_xpk.hh | |
| Resonance.cc | |
| Resonance.fwd.hh | |
| Resonance.hh | |
| ResonanceList.cc | |
| ResonanceList.fwd.hh | |
| ResonanceList.hh | Table with atomID - chemical shift mapping |
| StructureDependentPeakCalibrator.cc | |
| StructureDependentPeakCalibrator.hh | |
| StructureIndependentPeakCalibrator.cc | |
| StructureIndependentPeakCalibrator.hh | |
| util.cc | |
| util.hh | |
| ► nonlocal | |
| BiasedFragmentMover.cc | |
| BiasedFragmentMover.fwd.hh | |
| BiasedFragmentMover.hh | |
| Chunk.cc | |
| Chunk.fwd.hh | |
| Chunk.hh | |
| HelixRotate.cc | |
| HelixRotate.fwd.hh | |
| HelixRotate.hh | |
| Policy.fwd.hh | |
| Policy.hh | |
| PolicyFactory.cc | |
| PolicyFactory.hh | |
| Region.cc | |
| Region.fwd.hh | |
| Region.hh | |
| SheetTranslate.cc | |
| SheetTranslate.fwd.hh | |
| SheetTranslate.hh | |
| SimpleTreeBuilder.cc | |
| SimpleTreeBuilder.fwd.hh | |
| SimpleTreeBuilder.hh | |
| SingleFragmentMover.cc | |
| SingleFragmentMover.fwd.hh | |
| SingleFragmentMover.hh | |
| SingleFragmentMoverCreator.cc | |
| SingleFragmentMoverCreator.hh | |
| SmoothPolicy.cc | |
| SmoothPolicy.hh | |
| StarTreeBuilder.cc | |
| StarTreeBuilder.fwd.hh | |
| StarTreeBuilder.hh | |
| TreeBuilder.fwd.hh | |
| TreeBuilder.hh | |
| TreeBuilderFactory.cc | |
| TreeBuilderFactory.hh | |
| UniformPolicy.cc | |
| UniformPolicy.hh | |
| util.cc | |
| util.hh | |
| ► normalmode | |
| NormalMode.cc | |
| NormalMode.hh | Initialization for NormalMode |
| NormalModeMinimizer.cc | High-level atom tree minimizer class |
| NormalModeMinimizer.fwd.hh | Protocols::normalmode::NormalModeMinimizer forward declarations |
| NormalModeMinimizer.hh | |
| NormalModeMinimizerCreator.hh | |
| NormalModeMultiFunc.cc | |
| NormalModeMultiFunc.hh | |
| NormalModeRelaxMover.cc | Normal Mode Perturbation + Relax |
| NormalModeRelaxMover.fwd.hh | Initialization for NormalMode |
| NormalModeRelaxMover.hh | Initialization for NormalMode |
| ► optimize_weights | |
| DDGBindOptEData.cc | |
| DDGBindOptEData.fwd.hh | Forward header for a optE position data class that holds interface ddG information |
| DDGBindOptEData.hh | Header file for OptEPositionData class that hold interface ddG information |
| DGBindOptEData.cc | Implementation of the OptEPositionData class that handles interface ddG optimization |
| DGBindOptEData.fwd.hh | |
| DGBindOptEData.hh | |
| IterativeOptEDriver.cc | Implementation of iterative weight fitting protocol |
| IterativeOptEDriver.fwd.hh | Forward declaration of iterative weight fitting protocol |
| IterativeOptEDriver.hh | A class for optimizing weights in an iterative weight fitting, sequence recovery test protocol |
| NestedEnergyTermOptEData.cc | |
| NestedEnergyTermOptEData.fwd.hh | Forward header for some special optE position data classes |
| NestedEnergyTermOptEData.hh | Classes to store by-energy-term rotamer data for optE, when using the unfolded state energy term |
| OptEData.cc | |
| OptEData.fwd.hh | Forward declarations for OptE data structures |
| OptEData.hh | |
| OptEMultifunc.cc | |
| OptEMultifunc.fwd.hh | |
| OptEMultifunc.hh | |
| PNatLigPoseOptEData.cc | |
| PNatLigPoseOptEData.fwd.hh | |
| PNatLigPoseOptEData.hh | |
| ► outputter | |
| FormatStringOutputter.cc | An abstract base class that implements format string parsing |
| FormatStringOutputter.fwd.hh | An abstract base class that implements format string parsing |
| FormatStringOutputter.hh | An abstract base class that implements format string parsing |
| Outputter.cc | An outputter can take a PipeMapSP, a PipeSP, or a PoseSP and write it to a file |
| Outputter.fwd.hh | An outputter can take a PipeMapSP, a PipeSP, or a PoseSP and write it to a file |
| Outputter.hh | An outputter can take a PipeMapSP, a PipeSP, or a PoseSP and write it to a file |
| PDBOutputter.cc | An outputter can take a PipeMapSP, a PipeSP, or a PoseSP and write it to a pdb |
| PDBOutputter.fwd.hh | An outputter can take a PipeMapSP, a PipeSP, or a PoseSP and write it to a pdb |
| PDBOutputter.hh | An outputter can take a PipeMapSP, a PipeSP, or a PoseSP and write it to a pdb |
| ResFileOutputter.cc | Saves a resfile that is generated by applying the input task operations to the pose |
| ResFileOutputter.fwd.hh | Saves a resfile that is generated by applying the input task operations to the pose |
| ResFileOutputter.hh | Saves a resfile that is generated by applying the input task operations to the pose |
| SilentFileOutputter.cc | An outputter can take a PipeMapSP, a PipeSP, or a PoseSP and write it to a pdb |
| SilentFileOutputter.fwd.hh | An outputter can take a PipeMapSP, a PipeSP, or a PoseSP and write it to a silent file (or many!) |
| SilentFileOutputter.hh | An outputter can take a PipeMapSP, a PipeSP, or a PoseSP and write it to a silent file( or many! ) |
| ► pack_daemon | |
| DynamicAggregateFunction.cc | |
| DynamicAggregateFunction.fwd.hh | |
| DynamicAggregateFunction.hh | Declaration for a file-driven definition for the active states in a multistate design and the set of mathematical expressions that together define the fitness function for the sequence being designed |
| EntityCorrespondence.cc | Implementation for class EntityCorrespondence |
| EntityCorrespondence.fwd.hh | |
| EntityCorrespondence.hh | Forward declaration for class EntityCorrespondence |
| MultistateAggregateFunction.cc | Implementation for class MultistateAggregateFunction to work with the PackDeamon classes (not to be confused with J. Ashworth's MultiStateAggregateFunction class) |
| MultistateAggregateFunction.fwd.hh | Forward declaration of class MultistateAggregateFunction |
| MultistateAggregateFunction.hh | Declaration for class MultistateAggregateFunction to work with the PackDeamon classes (not to be confused with J. Ashworth's MultiStateAggregateFunction class) |
| MultistateFitnessFunction.cc | Implementation of the class MultistateFitnessFunction |
| MultistateFitnessFunction.fwd.hh | Forward declaration of class MultistateFitnessFunction |
| MultistateFitnessFunction.hh | Declaration for class MultistateFitnessFunction to work with the PackDeamon classes (not to be confused with J. Ashworth's MultiStateFitnessFunction class) |
| PackDaemon.cc | Implementation for class PackDaemon |
| PackDaemon.fwd.hh | |
| PackDaemon.hh | Declaration for class PackDaemon |
| util.cc | Utility functions for working with the multistate-design classes |
| util.hh | Declaration for utility functions for working with the multistate-design classes |
| ► pb_potential | |
| SetupPoissonBoltzmannPotential.cc | |
| SetupPoissonBoltzmannPotential.fwd.hh | |
| SetupPoissonBoltzmannPotential.hh | |
| SetupPoissonBoltzmannPotentialCreator.hh | |
| ► pmut_scan | |
| AlterSpecDisruptionDriver.cc | A protocol that tries to find interface-disrupting mutations as phase 1 of an altered-specificity protocol |
| AlterSpecDisruptionDriver.hh | A protocol that tries to find interface-disrupting mutations as phase 1 of an altered-specificity protocol |
| Mutant.cc | A helper class for the point mut scan protocol which holds data about mutants |
| Mutant.fwd.hh | Forward declaration for Mutant.hh |
| Mutant.hh | A helper class for the point mut scan protocol |
| PointMutScanDriver.cc | A protocol that tries to find stability enhancing mutations |
| PointMutScanDriver.hh | A protocol that tries to find stability enhancing mutations |
| ► pockets | |
| DarcElectrostatics.cc | |
| DarcElectrostatics.fwd.hh | Protocols::pockets::DarcElectrostatics forward declarations header |
| DarcElectrostatics.hh | |
| DarcParticleSwarmMinimizer.cc | |
| DarcParticleSwarmMinimizer.fwd.hh | |
| DarcParticleSwarmMinimizer.hh | |
| Fingerprint.cc | Protocols::pockets::Fingerprint functions |
| Fingerprint.fwd.hh | Protocols::pockets::Fingerprint forward declarations header |
| Fingerprint.hh | Protocols::pockets::Fingerprint header |
| FingerprintMultifunc.cc | |
| FingerprintMultifunc.fwd.hh | Protocols::pockets::FingerprintMultifunc forward declarations |
| FingerprintMultifunc.hh | Fingerprint multifunction class |
| PocketConstraint.cc | |
| PocketConstraint.fwd.hh | Core::grid::Pockets::PocketConstraint forward declarations header |
| PocketConstraint.hh | |
| PocketConstraintCreator.hh | |
| PocketExemplarMultifunc.cc | |
| PocketExemplarMultifunc.fwd.hh | Protocols::pockets::PocketExemplarMultifunc forward declarations |
| PocketExemplarMultifunc.hh | Pocket multifunction class |
| PocketGrid.cc | Protocols::pockets::PocketGrid functions |
| PocketGrid.fwd.hh | Protocols::pockets::PocketGrid forward declarations header |
| PocketGrid.hh | Protocols::pockets::PocketGrid header |
| ► pose_reporters | |
| BasicPosePropertyReporterCreators.hh | Collection of PosePropertySelector creators for basic pose reporters |
| BasicPosePropertyReporters.cc | |
| BasicPosePropertyReporters.hh | Collection of simple pose property reporters |
| ► pose_selectors | |
| BasicPoseSelectorCreators.hh | Collection of PoseSelector creators for basic selectors |
| BasicPoseSelectors.cc | |
| BasicPoseSelectors.hh | Collection of simple pose selectors |
| ClusterPosePropertyReporter.cc | |
| ClusterPoseSelector.cc | |
| ClusterPoseSelector.hh | Cluster pose selector using protocols::cluster |
| ClusterPoseSelectorCreator.hh | Creator for ClusterPoseSelector |
| ► protein_interface_design | |
| ► filters | |
| AtomicContactCountFilter.cc | |
| AtomicContactCountFilter.fwd.hh | Forward declaration for AtomicContactCountFilter |
| AtomicContactCountFilter.hh | |
| AtomicContactCountFilterCreator.hh | FilterCreators for the AtomicContactCountFilter |
| AverageDegreeFilter.cc | |
| AverageDegreeFilter.fwd.hh | Forward declaration for AverageDegreeFilter |
| AverageDegreeFilter.hh | |
| AverageDegreeFilterCreator.hh | FilterCreators for the AverageDegreeFilter |
| BindingStrainFilter.cc | |
| BindingStrainFilter.fwd.hh | Forward declaration for BindingStrainFilter |
| BindingStrainFilter.hh | |
| BindingStrainFilterCreator.hh | FilterCreators for the BindingStrainFilter |
| BoltzmannFilter.cc | |
| BoltzmannFilter.fwd.hh | Forward declaration for BoltzmannFilter |
| BoltzmannFilter.hh | |
| BoltzmannFilterCreator.hh | FilterCreators for the BoltzmannFilter |
| ClashWithTargetFilter.cc | ClashWithTarget filtering |
| ClashWithTargetFilter.hh | Clash check with Target using motifgrafting |
| ClashWithTargetFilterCreator.hh | FilterCreators for the ClashWithTargetFilter |
| DesignableResiduesFilter.cc | |
| DesignableResiduesFilter.fwd.hh | Forward declaration for DesignableResiduesFilter |
| DesignableResiduesFilter.hh | |
| DesignableResiduesFilterCreator.hh | FilterCreators for the DesignableResiduesFilter |
| DisulfideFilter.cc | |
| DisulfideFilter.hh | |
| DisulfideFilterCreator.hh | FilterCreators for the DisulfideFilter |
| FilterScan.cc | |
| FilterScan.fwd.hh | Forward declaration for FilterScanFilter |
| FilterScan.hh | |
| FilterScanCreator.hh | FilterCreators for the FilterScanFilter |
| FNatFilter.cc | Filtering on fraction of native contacts |
| FNatFilter.hh | Calculate L_RMSD using the method from protocols::docking::metrics |
| FNatFilterCreator.hh | FilterCreators for the FNatFilter |
| HbondsToAtomFilter.cc | |
| HbondsToAtomFilter.fwd.hh | Forward declaration for HbondsToAtomFilter |
| HbondsToAtomFilter.hh | Definition of filter classes for iterations of docking/design |
| HbondsToAtomFilterCreator.hh | FilterCreators for the filters defined in HbondsToAtomFilterCreator.hh |
| HbondsToResidueFilter.cc | |
| HbondsToResidueFilter.fwd.hh | Forward declaration for HbondsToResidueFilter |
| HbondsToResidueFilter.hh | Definition of filter classes for iterations of docking/design |
| HbondsToResidueFilterCreator.hh | FilterCreators for the filters defined in HbondsToResidueFilterCreator.hh |
| InterfaceHolesFilter.cc | Find packing defects at an interface using packstat score terms |
| InterfaceHolesFilter.hh | Find packing defects at an interface using packstat score terms |
| InterfaceHolesFilterCreator.hh | FilterCreators for the InterfaceHolesFilter |
| IRmsdFilter.cc | |
| IRmsdFilter.hh | Calculate I_RMSD using the method from protocols::docking::metrics |
| IRmsdFilterCreator.hh | FilterCreators for the IRmsdFilter |
| LRmsdFilter.cc | |
| LRmsdFilter.hh | Calculate L_RMSD using the method from protocols::docking::metrics |
| LRmsdFilterCreator.hh | FilterCreators for the LRmsdFilter |
| RelativeSegmentFilter.cc | |
| RelativeSegmentFilter.fwd.hh | Forward declaration for RelativeSegmentFilter |
| RelativeSegmentFilter.hh | |
| RelativeSegmentFilterCreator.hh | FilterCreators for the filters defined in RelativeSegmentFilterCreator.hh |
| RmsdFilter.cc | Rmsd filtering |
| RmsdFilter.hh | Find packing defects at an interface using packstat score terms |
| RmsdFilterCreator.hh | FilterCreators for the RmsdFilter |
| SequenceRecoveryFilter.cc | |
| SequenceRecoveryFilter.fwd.hh | Forward declaration for SequenceRecoveryFilter |
| SequenceRecoveryFilter.hh | |
| SequenceRecoveryFilterCreator.hh | FilterCreators for the SequenceRecoveryFilter |
| SpecificResiduesNearInterfaceFilter.cc | |
| SpecificResiduesNearInterfaceFilter.fwd.hh | Forward header for SpecificResiduesNearInterface |
| SpecificResiduesNearInterfaceFilter.hh | |
| SpecificResiduesNearInterfaceFilterCreator.hh | Pass if a specific set of residues are near the interface |
| StubScoreFilter.cc | |
| StubScoreFilter.fwd.hh | Forward declaration for StubScoreFilter |
| StubScoreFilter.hh | |
| StubScoreFilterCreator.hh | FilterCreators for the StubScoreFilter |
| StubScoreFilterLoops.hh | |
| StubScoreLoopsFilter.cc | |
| StubScoreLoopsFilter.fwd.hh | Forward declaration for StubScoreLoopsFilter |
| StubScoreLoopsFilter.hh | |
| StubScoreLoopsFilterCreator.hh | FilterCreators for the StubScoreLoopsFilter |
| TorsionFilter.cc | |
| TorsionFilter.fwd.hh | |
| TorsionFilter.hh | |
| TorsionFilterCreator.hh | |
| ► movers | |
| AddChainBreak.cc | |
| AddChainBreak.hh | |
| AddChainBreakCreator.hh | Declaration of the MoverCreator class for the AddChainBreak |
| AddSidechainConstraintsToHotspots.cc | |
| AddSidechainConstraintsToHotspots.hh | |
| AddSidechainConstraintsToHotspotsCreator.hh | Declaration of the MoverCreator class for the AddSidechainConstraintsToHotspots |
| BackrubDDMover.cc | |
| BackrubDDMover.hh | Derived class from mover for dock design with backrub moves |
| BackrubDDMoverCreator.hh | Declaration of the MoverCreator class for the BackrubDDMover |
| BestHotspotCstMover.cc | |
| BestHotspotCstMover.hh | |
| BestHotspotCstMoverCreator.hh | Declaration of the MoverCreator class for the BestHotspotCstMover |
| BuildAlaPose.cc | |
| BuildAlaPose.fwd.hh | |
| BuildAlaPose.hh | |
| BuildAlaPoseCreator.hh | Declaration of the MoverCreator class for the BuildAlaPose |
| DesignMinimizeHbonds.cc | |
| DesignMinimizeHbonds.hh | |
| DesignMinimizeHbondsCreator.hh | Declaration of the MoverCreator class for the DesignMinimizeHbonds |
| DisulfideMover.cc | |
| DisulfideMover.hh | |
| DisulfideMoverCreator.hh | Declaration of the MoverCreator class for the DisulfideMover |
| DockAndRetrieveSidechains.cc | |
| DockAndRetrieveSidechains.hh | |
| DockAndRetrieveSidechainsCreator.hh | Declaration of the MoverCreator class for the DockAndRetrieveSidechains |
| DockWithHotspotMover.cc | |
| DockWithHotspotMover.fwd.hh | |
| DockWithHotspotMover.hh | |
| DockWithHotspotMoverCreator.hh | This class will create instances of protocols::moves::Mover DockWithHotspotMover for the protocols::moves::MoverFactory |
| FavorNativeResiduePreCycle.cc | |
| FavorNativeResiduePreCycle.hh | |
| FavorNativeResiduePreCycleCreator.hh | Declaration of the MoverCreator class for the FavorNativeResiduePreCycle |
| FavorNonNativeResiduePreCycle.cc | |
| FavorNonNativeResiduePreCycle.hh | |
| FavorNonNativeResiduePreCycleCreator.hh | |
| HotspotDisjointedFoldTreeMover.cc | |
| HotspotDisjointedFoldTreeMover.hh | |
| HotspotDisjointedFoldTreeMoverCreator.hh | Declaration of the MoverCreator class for the HotspotDisjointedFoldTreeMover |
| HotspotHasherMover.cc | |
| HotspotHasherMover.hh | |
| HotspotHasherMoverCreator.hh | Declaration of the MoverCreator class for the HotspotHasherMover |
| InterfaceRecapitulationMover.cc | |
| InterfaceRecapitulationMover.hh | |
| InterfaceRecapitulationMoverCreator.hh | Declaration of the MoverCreator class for the InterfaceRecapitulationMover |
| LoopFinder.cc | |
| LoopFinder.hh | Header for class to find loops (parseable options to control how loops are found) |
| LoopFinderCreator.hh | Declaration of the MoverCreator class for the LoopFinder |
| LoopLengthChange.cc | |
| LoopLengthChange.fwd.hh | |
| LoopLengthChange.hh | |
| LoopLengthChangeCreator.hh | Declaration of the MoverCreator class for the LoopLengthChange |
| LoopMoverFromCommandLine.cc | |
| LoopMoverFromCommandLine.fwd.hh | |
| LoopMoverFromCommandLine.hh | |
| LoopMoverFromCommandLineCreator.hh | |
| LoopOver.cc | |
| LoopOver.hh | |
| LoopOverCreator.hh | Declaration of the MoverCreator class for the LoopOver |
| LoopRemodel.cc | Parseable class to run loop perturbation or refinement between a given loop between start/end (inclusive). Intended to sample loop conformations at an interface |
| LoopRemodel.fwd.hh | |
| LoopRemodel.hh | Header for parseable class to run loop perturbation or refinement between a given loop between start/end (inclusive) |
| LoopRemodelCreator.hh | Declaration of the MoverCreator class for the LoopRemodel |
| MapHotspot.cc | |
| MapHotspot.hh | |
| MapHotspotCreator.hh | Declaration of the MoverCreator class for the MapHotspot |
| NullDesignMover.cc | |
| NullDesignMover.hh | |
| PatchdockTransform.cc | |
| PatchdockTransform.fwd.hh | |
| PatchdockTransform.hh | |
| PatchdockTransformCreator.hh | Declaration of the MoverCreator class for the PatchdockTransform |
| PeptideStapleDesignMover.cc | |
| PeptideStapleDesignMover.hh | |
| PeptideStapleDesignMoverCreator.hh | Declaration of the MoverCreator class for the PeptideStapleDesignMover |
| PlacementAuctionMover.cc | |
| PlacementAuctionMover.fwd.hh | Forward declations for PlacementAuctionMover |
| PlacementAuctionMover.hh | Definition of a class for making the placement auction used by PlaceSimultaneouslyMover |
| PlacementAuctionMoverCreator.hh | Declaration of the MoverCreator class for the PlacementAuctionMover |
| PlacementMinimizationMover.cc | |
| PlacementMinimizationMover.fwd.hh | Forward declations for PlacementMinimizationMover |
| PlacementMinimizationMover.hh | Definition of a class for making the placement auction used by PlaceSimultaneouslyMover |
| PlacementMinimizationMoverCreator.hh | Declaration of the MoverCreator class for the PlacementMinimizationMover |
| PlaceOnLoop.cc | |
| PlaceOnLoop.fwd.hh | |
| PlaceOnLoop.hh | |
| PlaceOnLoopCreator.hh | Declaration of the MoverCreator class for the PlaceOnLoop |
| PlaceSimultaneouslyMover.cc | |
| PlaceSimultaneouslyMover.hh | |
| PlaceSimultaneouslyMoverCreator.hh | Declaration of the MoverCreator class for the PlaceSimultaneouslyMover |
| PlaceStubMover.cc | |
| PlaceStubMover.fwd.hh | Forward declarations for PlaceStubMover |
| PlaceStubMover.hh | Definition of classes for grafting hotspots into a pose |
| PlaceStubMoverCreator.hh | Declaration of the MoverCreator class for the PlaceStubMover |
| PlaceUtils.cc | Collection of utility functions for placement classes |
| PlaceUtils.hh | |
| PrepackMover.cc | |
| PrepackMover.hh | |
| PrepackMoverCreator.hh | Declaration of the MoverCreator class for the PrepackMover |
| ProteinInterfaceMultiStateDesignMover.cc | |
| ProteinInterfaceMultiStateDesignMover.fwd.hh | |
| ProteinInterfaceMultiStateDesignMover.hh | |
| ProteinInterfaceMultiStateDesignMoverCreator.hh | Declaration of the MoverCreator class for the ProteinInterfaceMultiStateDesignMover |
| RandomMutation.cc | |
| RandomMutation.fwd.hh | |
| RandomMutation.hh | |
| RandomMutationCreator.hh | Declaration of the MoverCreator class for the RandomMutation |
| RepackMinimize.cc | |
| RepackMinimize.hh | |
| RepackMinimizeCreator.hh | Declaration of the MoverCreator class for the RepackMinimize |
| SaveAndRetrieveSidechains.cc | |
| SaveAndRetrieveSidechains.fwd.hh | |
| SaveAndRetrieveSidechains.hh | |
| SaveAndRetrieveSidechainsCreator.hh | Declaration of the MoverCreator class for the SaveAndRetrieveSidechains |
| SetAtomTree.cc | |
| SetAtomTree.hh | |
| SetAtomTreeCreator.hh | Declaration of the MoverCreator class for the SetAtomTree |
| SetTemperatureFactor.cc | |
| SetTemperatureFactor.fwd.hh | |
| SetTemperatureFactor.hh | |
| SetTemperatureFactorCreator.hh | Declaration of the MoverCreator class for the SetTemperatureFactor |
| SetupHotspotConstraintsLoopsMover.cc | |
| SetupHotspotConstraintsLoopsMover.fwd.hh | |
| SetupHotspotConstraintsLoopsMover.hh | |
| SetupHotspotConstraintsLoopsMoverCreator.hh | Declaration of the MoverCreator class for the SetupHotspotConstraintsLoopsMover |
| SetupHotspotConstraintsMover.cc | |
| SetupHotspotConstraintsMover.fwd.hh | |
| SetupHotspotConstraintsMover.hh | |
| SetupHotspotConstraintsMoverCreator.hh | Declaration of the MoverCreator class for the SetupHotspotConstraintsMover |
| ShoveResidueMover.cc | |
| ShoveResidueMover.hh | |
| ShoveResidueMoverCreator.hh | Declaration of the MoverCreator class for the ShoveResidueMover |
| SpinMover.cc | |
| SpinMover.hh | |
| SpinMoverCreator.hh | Declaration of the MoverCreator class for the SpinMover |
| SubroutineMover.cc | |
| SubroutineMover.fwd.hh | Forward declations for SubroutineMover |
| SubroutineMover.hh | Definition of a class for making the placement auction used by PlaceSimultaneouslyMover |
| SubroutineMoverCreator.hh | Declaration of the MoverCreator class for the SubroutineMover |
| TaskAwareCsts.cc | |
| TaskAwareCsts.fwd.hh | |
| TaskAwareCsts.hh | |
| TaskAwareCstsCreator.hh | Declaration of the MoverCreator class for the TaskAwareCsts |
| TopologyBrokerMover.cc | |
| TopologyBrokerMover.fwd.hh | |
| TopologyBrokerMover.hh | |
| TopologyBrokerMoverCreator.hh | This class will create instances of protocols::moves::Mover TopologyBrokerMover for the protocols::moves::MoverFactory |
| TryRotamers.cc | |
| TryRotamers.hh | |
| TryRotamersCreator.hh | Declaration of the MoverCreator class for the TryRotamers |
| VLB.cc | |
| VLB.hh | |
| VLBCreator.hh | Declaration of the MoverCreator class for the VLB |
| design_utils.cc | |
| design_utils.hh | |
| DockDesignFilterFactory.cc | |
| DockDesignFilterFactory.fwd.hh | |
| DockDesignFilterFactory.hh | |
| parse_filters.cc | |
| ParserJobInputter.cc | |
| ParserJobInputter.fwd.hh | |
| ParserJobInputter.hh | |
| ParserJobInputterCreator.hh | |
| PatchdockReader.fwd.hh | |
| read_patchdock.cc | |
| read_patchdock.hh | |
| ReportPSSMDifference.cc | |
| ReportPSSMDifference.fwd.hh | |
| ReportPSSMDifference.hh | |
| util.cc | |
| util.hh | |
| ► qsar | |
| ► scoring_grid | |
| AtrGrid.cc | |
| AtrGrid.fwd.hh | |
| AtrGrid.hh | |
| AtrGridCreator.hh | |
| ChargeGrid.cc | This is an implementation of equation 3 in Goodford, J. Med. Chem. 1985,28,849-857. doi:10.1021/jm00145a002 |
| ChargeGrid.fwd.hh | |
| ChargeGrid.hh | This is an implementation of equation 3 in Goodford, J. Med. Chem. 1985,28,849-857. doi:10.1021/jm00145a002 |
| ChargeGridCreator.hh | |
| ClassicGrid.cc | |
| ClassicGrid.fwd.hh | |
| ClassicGrid.hh | |
| ClassicGridCreator.hh | |
| ConstantScoreBase.fwd.hh | |
| ConstantScoreBase.hh | This is a base class for defining constant terms which are computed over an entire ligand rather than on a per atom basis The unneeded functions are stubbed out, everything left is pure virtual |
| GridBase.fwd.hh | |
| GridBase.hh | |
| GridCreator.cc | |
| GridCreator.hh | Base class for GridCreators for the Grid load time factory registration scheme |
| GridFactory.cc | |
| GridFactory.fwd.hh | |
| GridFactory.hh | |
| GridInitMover.cc | |
| GridInitMover.fwd.hh | |
| GridInitMover.hh | |
| GridInitMoverCreator.hh | |
| GridManager.cc | |
| GridManager.fwd.hh | |
| GridManager.hh | |
| HbaGrid.cc | |
| HbaGrid.fwd.hh | |
| HbaGrid.hh | |
| HbaGridCreator.hh | |
| HbdGrid.cc | |
| HbdGrid.fwd.hh | |
| HbdGrid.hh | |
| HbdGridCreator.hh | |
| LigandPropertyScore.cc | |
| LigandPropertyScore.fwd.hh | |
| LigandPropertyScore.hh | |
| LigandPropertyScoreCreator.hh | |
| RepGrid.cc | |
| RepGrid.fwd.hh | |
| RepGrid.hh | |
| RepGridCreator.hh | |
| ScoreNormalization.cc | Header file for Score Normalization methods |
| ScoreNormalization.fwd.hh | Report data to database |
| ScoreNormalization.hh | Header file for Score Normalization methods |
| ScoringGridLoader.cc | |
| ScoringGridLoader.fwd.hh | |
| ScoringGridLoader.hh | |
| ScoringGridLoaderCreator.hh | Creator classes for the default DataLoader classes, TaskOperationLoader and ScoreFunctionLoader |
| ShapeGrid.cc | |
| ShapeGrid.fwd.hh | |
| ShapeGrid.hh | |
| ShapeGridCreator.hh | |
| SingleGrid.cc | |
| SingleGrid.fwd.hh | |
| SingleGrid.hh | |
| SolvationGrid.cc | |
| SolvationGrid.fwd.hh | |
| SolvationGrid.hh | |
| SolvationGridCreator.hh | |
| SolvationMetaGrid.cc | |
| SolvationMetaGrid.fwd.hh | |
| SolvationMetaGrid.hh | |
| SolvationMetaGridCreator.hh | |
| VdwGrid.cc | |
| VdwGrid.fwd.hh | |
| VdwGrid.hh | |
| VdwGridCreator.hh | |
| qsarMap.cc | |
| qsarMap.fwd.hh | |
| qsarMap.hh | |
| qsarMover.cc | |
| qsarMover.fwd.hh | |
| qsarMover.hh | |
| qsarMoverCreator.hh | |
| qsarOptFunc.cc | |
| qsarOptFunc.fwd.hh | |
| qsarOptFunc.hh | |
| RenderGridsToKinemage.cc | |
| RenderGridsToKinemage.fwd.hh | |
| RenderGridsToKinemage.hh | |
| RenderGridsToKinemageCreator.hh | |
| ► rbsegment_relax | |
| AutoRBRelaxMover.cc | |
| AutoRBRelaxMover.hh | |
| FragInsertAndAlignMover.cc | |
| FragInsertAndAlignMover.hh | |
| IdealizeHelices.cc | Protocols for folding into density |
| IdealizeHelices.hh | |
| IdealizeHelicesCreator.hh | |
| MakeStarTopology.cc | Protocols for folding into density |
| MakeStarTopology.hh | |
| MakeStarTopologyCreator.hh | |
| OptimizeThreading.cc | Protocols for folding into density |
| OptimizeThreading.hh | |
| OptimizeThreadingCreator.hh | |
| RBSegment.cc | |
| RBSegment.fwd.hh | |
| RBSegment.hh | |
| RBSegmentMover.cc | |
| RBSegmentMover.hh | |
| RBSegmentRelax.cc | RBSegmentRelax protocol |
| RBSegmentRelax.hh | RBSegmentRelax protocol |
| RBSegmentRelax_main.cc | |
| RBSegmentRelax_main.hh | |
| util.cc | |
| util.hh | |
| ► relax | |
| AtomCoordinateCstMover.cc | Add coordinate constraints to a pose, as for the relax protocol |
| AtomCoordinateCstMover.fwd.hh | |
| AtomCoordinateCstMover.hh | Coordinate constraints for relax, etc |
| AtomCoordinateCstMoverCreator.hh | |
| CentroidRelax.cc | |
| CentroidRelax.fwd.hh | |
| CentroidRelax.hh | Centroid-based relax, using Frank Dimaio's updated centroid statistics |
| ClassicRelax.cc | |
| ClassicRelax.hh | |
| cst_util.cc | |
| cst_util.hh | Set of functions for adding constraints used in relax |
| FastRelax.cc | The FastRelax Protocol |
| FastRelax.fwd.hh | |
| FastRelax.hh | The FastRelax Protocol |
| FastRelaxCreator.hh | |
| MiniRelax.cc | |
| MiniRelax.fwd.hh | Forward declaration for MiniRelax class |
| MiniRelax.hh | |
| Ramady.cc | Header for the Rana energy repair code, Ramady |
| Ramady.hh | Header for the Rana energy repair code, Ramady |
| relax_main.cc | |
| relax_main.hh | |
| RelaxProtocolBase.cc | |
| RelaxProtocolBase.fwd.hh | |
| RelaxProtocolBase.hh | |
| util.cc | Initialization protocols for relax and utility functions |
| util.hh | Initialization protocols for relax and utility functions |
| WorkUnit_BatchRelax.cc | |
| WorkUnit_BatchRelax.hh | |
| ► rigid | |
| PoseMembraneRigidBodyMover.cc | |
| PoseMembraneRigidBodyMover.hh | |
| RB_geometry.cc | |
| RB_geometry.hh | |
| rigid_body_moves.cc | |
| rigid_body_moves.hh | |
| RigidBodyMotionMover.cc | |
| RigidBodyMotionMover.fwd.hh | |
| RigidBodyMotionMover.hh | |
| RigidBodyMover.cc | |
| RigidBodyMover.fwd.hh | RigidBodyMover forward declarations header |
| RigidBodyMover.hh | |
| RigidBodyMoverCreator.hh | This class will create instances of Movers SmallMover and ShearMover for the MoverFactory |
| RollMover.cc | |
| RollMover.fwd.hh | RollMover forward declarations header |
| RollMover.hh | |
| RollMoverCreator.hh | This class will create instances of Mover RollMover for the MoverFactory |
| RotateJumpAxisMover.cc | RotateJumpAxisMover methods implemented |
| RotateJumpAxisMover.fwd.hh | RotateJumpAxisMover forward declarations header |
| RotateJumpAxisMover.hh | RotateJumpAxisMover header |
| ► rosetta_scripts | |
| MultipleOutputWrapper.cc | This mover wraps another mover or a ROSETTASCRIPTS block to obtain additional, |
| MultipleOutputWrapper.hh | This mover wraps another mover or a ROSETTASCRIPTS block to obtain additional, |
| MultipleOutputWrapperCreator.hh | This class will create instances of Mover MultipleOutputWrapper for the MoverFactory |
| MultiplePoseMover.cc | This mover accepts multiple poses from a previous mover, performs selection using a provided pose selector, applies contained ROSETTASCRIPTS protocol (ParsedProtocol), and output multiple poses to the next mover of JD2 |
| MultiplePoseMover.hh | This mover accepts multiple poses from a previous mover, performs selection using a provided pose selector, applies contained ROSETTASCRIPTS protocol (ParsedProtocol), and output multiple poses to the next mover of JD2 |
| MultiplePoseMoverCreator.hh | This class will create instances of Mover MultiplePoseMover for the MoverFactory |
| ParsedProtocol.cc | A mover that applies a protocol parsed from a ROSETTASCRIPTS script |
| ParsedProtocol.fwd.hh | Forward declarations for ParsedProtocol |
| ParsedProtocol.hh | |
| ParsedProtocolCreator.hh | This class will create instances of Mover DockDesign for the MoverFactory |
| PosePropertyReporter.cc | |
| PosePropertyReporter.fwd.hh | |
| PosePropertyReporter.hh | Base class for pose selectors used by MultiplePoseMover |
| PosePropertyReporterCreator.cc | Base class for PosePropertyReporters for the load-time factory registration scheme |
| PosePropertyReporterCreator.hh | Base class for PosePropertyReporters for the load-time factory registration scheme |
| PosePropertyReporterFactory.cc | Factory for PosePropertyReporters |
| PosePropertyReporterFactory.fwd.hh | Factory for PosePropertyReporters forward definitions |
| PosePropertyReporterFactory.hh | Factory for PosePropertyReporters |
| PoseSelector.cc | |
| PoseSelector.fwd.hh | Forward declarations for PoseSelector |
| PoseSelector.hh | Base class for pose selectors used by MultiplePoseMover |
| PoseSelectorCreator.cc | |
| PoseSelectorCreator.hh | Base class for PoseSelectors for the load-time factory registration scheme |
| PoseSelectorFactory.cc | Factory for PoseSelectors |
| PoseSelectorFactory.fwd.hh | |
| PoseSelectorFactory.hh | |
| RosettaScriptsParser.cc | August 2008 job distributor as planned at RosettaCon08 - Interface base class Parser |
| RosettaScriptsParser.hh | Header file for Parser class, part of August 2008 job distributor |
| SavePoseMover.cc | |
| SavePoseMover.fwd.hh | |
| SavePoseMover.hh | |
| SavePoseMoverCreator.hh | This class will create instances of Mover SavePoseMover for the MoverFactory |
| util.cc | |
| util.hh | |
| ► rotamer_recovery | |
| RotamerRecovery.cc | |
| RotamerRecovery.fwd.hh | Measure how well rosetta is a recovering the conformation of an experimentally validated structure |
| RotamerRecovery.hh | |
| RotamerRecoveryCreator.cc | Creator classes for components of the RotamerRecovery framework |
| RotamerRecoveryCreator.fwd.hh | |
| RotamerRecoveryCreator.hh | |
| RotamerRecoveryFactory.cc | Factory for creating RotamerRecoverys objects |
| RotamerRecoveryFactory.fwd.hh | Report atom-atom pair geometry and scores to rotamer_recovery Statistics Scientific Benchmark |
| RotamerRecoveryFactory.hh | Factory for creating RotamerRecovery objects |
| RotamerRecoveryMover.cc | A wrapper that measures how similar the rotamers are between before and after running the child mover |
| RotamerRecoveryMover.fwd.hh | Measure how well rosetta is a recovering the conformation of an experimentally validated structure |
| RotamerRecoveryMover.hh | A wrapper that measures how similar the rotamers are between before and after running the child mover |
| RotamerRecoveryMoverCreator.hh | This class will create instances of Mover ConstraintSetMover for the MoverFactory |
| RRComparer.cc | |
| RRComparer.fwd.hh | Measure how well rosetta is a recovering the conformation of an experimentally validated structure |
| RRComparer.hh | |
| RRComparerAutomorphicRMSD.cc | |
| RRComparerAutomorphicRMSD.fwd.hh | Measure how well rosetta is a recovering the conformation of an experimentally validated structure by measuing the minimum root mean squared deviation of sidechain atoms for all chemical atomorphic forms |
| RRComparerAutomorphicRMSD.hh | |
| RRComparerElecDensDiff.cc | |
| RRComparerElecDensDiff.fwd.hh | Measure rotamer recovery by change in sidechain electron density correlation |
| RRComparerElecDensDiff.hh | |
| RRProtocol.cc | |
| RRProtocol.fwd.hh | Manage how the rotamer recovery test should be preformed |
| RRProtocol.hh | |
| RRProtocolMinPack.cc | |
| RRProtocolMinPack.fwd.hh | Preform the rotamer recovery test by minimizing each residue in a fixed context |
| RRProtocolMinPack.hh | |
| RRProtocolMover.cc | Preform the rotamer recovery after applying mover |
| RRProtocolMover.fwd.hh | Preform the rotamer recovery after applying mover |
| RRProtocolMover.hh | Preform the rotamer recovery after applying mover |
| RRProtocolPackRotamers.cc | |
| RRProtocolPackRotamers.fwd.hh | Preform the rotamer recovery test using the pack_rotamers discrete optimization algorithm |
| RRProtocolPackRotamers.hh | |
| RRProtocolReferenceStructure.cc | Preform the rotamer recovery against a reference structure |
| RRProtocolReferenceStructure.fwd.hh | Preform the rotamer recovery after applying mover |
| RRProtocolReferenceStructure.hh | Preform the rotamer recovery against a reference structure |
| RRProtocolRelax.cc | Perform the rotamer recovery test using the FastRelax protocol |
| RRProtocolRelax.fwd.hh | Perform the rotamer recovery test using the FastRelax protocol |
| RRProtocolRelax.hh | |
| RRProtocolRotamerTrials.cc | |
| RRProtocolRotamerTrials.fwd.hh | Preform the rotamer recovery test by determining the lowest energy (discrete) rotamer for each residue in a fixed context |
| RRProtocolRotamerTrials.hh | |
| RRProtocolRTMin.cc | |
| RRProtocolRTMin.fwd.hh | Preform the rotamer recovery test by minimizing each residue in a fixed context |
| RRProtocolRTMin.hh | |
| RRReporter.cc | |
| RRReporter.fwd.hh | |
| RRReporter.hh | |
| RRReporterHuman.cc | |
| RRReporterHuman.fwd.hh | Report how well rosetta is a recovering the conformation of an experimentally validated structure in a human readable format |
| RRReporterHuman.hh | |
| RRReporterSQLite.cc | |
| RRReporterSQLite.fwd.hh | Report Rotamer Recovery to an SQLite database |
| RRReporterSQLite.hh | |
| ► rotamer_sampler | |
| ► copy_dofs | |
| CopyDofRotamer.cc | |
| CopyDofRotamer.fwd.hh | |
| CopyDofRotamer.hh | |
| ResidueAlternativeRotamer.cc | |
| ResidueAlternativeRotamer.fwd.hh | |
| ResidueAlternativeRotamer.hh | |
| ResidueAlternativeRotamerComb.cc | |
| ResidueAlternativeRotamerComb.fwd.hh | |
| ResidueAlternativeRotamerComb.hh | |
| ResidueAlternativeSet.cc | |
| ResidueAlternativeSet.fwd.hh | |
| ResidueAlternativeSet.hh | |
| ResidueListRotamer.cc | |
| ResidueListRotamer.fwd.hh | |
| ResidueListRotamer.hh | |
| ► input_streams | |
| InputStreamRotamer.cc | |
| InputStreamRotamer.fwd.hh | |
| InputStreamRotamer.hh | |
| ► protein | |
| ProteinBetaAntiParallelRotamer.cc | |
| ProteinBetaAntiParallelRotamer.fwd.hh | |
| ProteinBetaAntiParallelRotamer.hh | |
| ProteinFragmentRotamer.cc | |
| ProteinFragmentRotamer.fwd.hh | |
| ProteinFragmentRotamer.hh | |
| ProteinMainChainRotamer.cc | |
| ProteinMainChainRotamer.fwd.hh | |
| ProteinMainChainRotamer.hh | |
| StepWiseBetaAntiParallelUtil.cc | |
| StepWiseBetaAntiParallelUtil.hh | |
| ► rigid_body | |
| EulerAngles.cc | |
| EulerAngles.fwd.hh | |
| EulerAngles.hh | |
| FloatingBaseUtil.cc | |
| FloatingBaseUtil.hh | |
| RigidBodyRotamer.cc | |
| RigidBodyRotamer.fwd.hh | |
| RigidBodyRotamer.hh | |
| RigidBodyRotamerValueRange.cc | |
| RigidBodyRotamerValueRange.fwd.hh | |
| RigidBodyRotamerValueRange.hh | |
| RigidBodyRotamerWithResidueAlternatives.cc | |
| RigidBodyRotamerWithResidueAlternatives.fwd.hh | |
| RigidBodyRotamerWithResidueAlternatives.hh | |
| RigidBodyRotamerWithResidueList.cc | |
| RigidBodyRotamerWithResidueList.fwd.hh | |
| RigidBodyRotamerWithResidueList.hh | |
| ► rna | |
| RNA_ChiRotamer.cc | Generate glycosidic chi rotamers for RNA |
| RNA_ChiRotamer.fwd.hh | Generate glycosidic chi rotamers for RNA |
| RNA_ChiRotamer.hh | Generate glycosidic chi rotamers for RNA |
| RNA_KicSampler.cc | Sample and torsions and close an RNA loop |
| RNA_KicSampler.fwd.hh | Sample and torsions and close an RNA loop |
| RNA_KicSampler.hh | |
| RNA_KinematicCloser.cc | Close a RNA loop with Kinematic Closer (KIC) |
| RNA_KinematicCloser.fwd.hh | Close a RNA loop with Kinematic Closer (KIC) |
| RNA_KinematicCloser.hh | Close a RNA loop with Kinematic Closer (KIC) |
| RNA_McMultiSuite.cc | Markov chain sampler for mulitple RNA suite |
| RNA_McMultiSuite.fwd.hh | Markov chain sampler for mulitple RNA suite |
| RNA_McMultiSuite.hh | Markov chain sampler for mulitple RNA suite |
| RNA_McSugar.cc | Markov chain sampler for sugar pucker |
| RNA_McSugar.fwd.hh | Markov chain sampler for sugar pucker |
| RNA_McSugar.hh | Markov chain sampler for sugar pucker |
| RNA_McSuite.cc | Markov chain sampler for RNA suite |
| RNA_McSuite.fwd.hh | Markov chain sampler for RNA suite |
| RNA_McSuite.hh | Markov chain sampler for RNA suite |
| RNA_NucleosideRotamer.cc | Generate rotamers for one RNA nucleoside (pucker + glycosidic chi) |
| RNA_NucleosideRotamer.fwd.hh | Generate rotamers for one RNA nucleoside (pucker + glycosidic chi) |
| RNA_NucleosideRotamer.hh | Generate rotamers for one RNA nucleoside (pucker + glycosidic chi) |
| RNA_RotamerSamplerUtil.cc | |
| RNA_RotamerSamplerUtil.fwd.hh | |
| RNA_RotamerSamplerUtil.hh | |
| RNA_SugarRotamer.cc | Generate sugar pucker rotamers for RNA |
| RNA_SugarRotamer.fwd.hh | Generate sugar pucker rotamers for RNA |
| RNA_SugarRotamer.hh | Generate sugar pucker rotamers for RNA |
| RNA_SuiteRotamer.cc | Generate rotamers for one RNA suite (from residue i to i+1) |
| RNA_SuiteRotamer.fwd.hh | Generate rotamers for one RNA suite (from residue i to i+1) |
| RNA_SuiteRotamer.hh | Generate rotamers for one RNA suite (from residue i to i+1) |
| ► screener | |
| RNA_TorsionScreener.cc | Screener checking whether the rna torsions are resonable |
| RNA_TorsionScreener.fwd.hh | |
| RNA_TorsionScreener.hh | |
| JumpRotamer.cc | |
| JumpRotamer.fwd.hh | |
| JumpRotamer.hh | |
| McComb.cc | Ensemble of Markov chain samplers for sampling combinatorially |
| McComb.fwd.hh | Ensemble of Markov chain samplers for sampling combinatorially |
| McComb.hh | Ensemble of Markov chain samplers for sampling combinatorially |
| McOneTorsion.cc | Markov chain sampler for one torsion |
| McOneTorsion.fwd.hh | Markov chain sampler for one torsion |
| McOneTorsion.hh | Markov chain sampler for one torsion |
| McRotamer.fwd.hh | Abstract Base Class for Markov chain rotamer sampler |
| McRotamer.hh | Abstract Base Class for Markov chain rotamer sampler |
| NoOpRotamer.cc | |
| NoOpRotamer.fwd.hh | |
| NoOpRotamer.hh | |
| RotamerAny.cc | Aggregate multiple samplers for sampling from any one of them |
| RotamerAny.fwd.hh | Aggregate multiple samplers for sampling from any one of them |
| RotamerAny.hh | Aggregate multiple samplers for sampling from any one of them |
| RotamerBase.fwd.hh | Abstract Base Class for Rotamer generator |
| RotamerBase.hh | Abstract Base Class for Rotamer generator |
| RotamerComb.cc | Aggregate of multiple rotamer samplers for sampling combinatorially |
| RotamerComb.fwd.hh | Aggregate of multiple rotamer samplers for sampling combinatorially |
| RotamerComb.hh | Aggregate of multiple rotamer samplers for sampling combinatorially |
| RotamerOneTorsion.cc | Generate rotamer for one torsion angle |
| RotamerOneTorsion.fwd.hh | Generate rotamer for one torsion angle |
| RotamerOneTorsion.hh | Generate rotamer for one torsion angle |
| RotamerOneValue.cc | |
| RotamerOneValue.fwd.hh | Generate rotamer for one torsion angle |
| RotamerOneValue.hh | Base class for RotamerOneValue |
| RotamerOneValueComb.cc | Aggregate of multiple rotamer samplers for sampling combinatorially |
| RotamerOneValueComb.fwd.hh | Aggregate of multiple rotamer samplers for sampling combinatorially |
| RotamerOneValueComb.hh | Aggregate of multiple rotamer samplers for sampling combinatorially |
| RotamerSized.cc | Aggregate multiple samplers for sampling from any one of them |
| RotamerSized.fwd.hh | Abstract Base Class for Rotamer generator with finite size |
| RotamerSized.hh | Abstract Base Class for Rotamer sampler with finite size |
| RotamerSizedAny.cc | Aggregate multiple samplers for sampling from any one of them |
| RotamerSizedAny.fwd.hh | Aggregate multiple samplers for sampling from any one of them |
| RotamerSizedAny.hh | Aggregate multiple samplers for sampling from any one of them |
| RotamerSizedComb.cc | Aggregate of multiple rotamer samplers for sampling combinatorially |
| RotamerSizedComb.fwd.hh | Aggregate of multiple rotamer samplers for sampling combinatorially |
| RotamerSizedComb.hh | Aggregate of multiple rotamer samplers for sampling combinatorially |
| RotamerType.hh | |
| ► RotamerDump | |
| RotamerDumpMover.cc | |
| RotamerDumpMover.fwd.hh | |
| RotamerDumpMover.hh | |
| ► rpc | |
| rpc.cc | |
| rpc.fwd.hh | JSON_RPC base classes |
| rpc.hh | |
| ► sasa_scores | |
| sasapack.cc | |
| sasapack.hh | Sasapack and other scores that are normalized by residue sasa |
| ► scoring | |
| ► methods | |
| ► pcs | |
| GridSearchIterator.cc | |
| GridSearchIterator.fwd.hh | |
| GridSearchIterator.hh | |
| PseudocontactShiftData.cc | |
| PseudocontactShiftData.fwd.hh | |
| PseudocontactShiftData.hh | |
| PseudocontactShiftEnergy.cc | |
| PseudocontactShiftEnergy.fwd.hh | |
| PseudocontactShiftEnergy.hh | |
| PseudocontactShiftEnergyCreator.hh | Declaration for the class that connects PseudocontactShiftEnergy with the ScoringManager |
| PseudocontactShiftInput.cc | |
| PseudocontactShiftInput.fwd.hh | |
| PseudocontactShiftInput.hh | |
| PseudocontactShiftTensor.cc | |
| PseudocontactShiftTensor.fwd.hh | |
| PseudocontactShiftTensor.hh | |
| TensorsOptimizer.cc | |
| TensorsOptimizer.fwd.hh | |
| TensorsOptimizer.hh | |
| ► pcs2 | |
| GridSearchIterator.cc | |
| GridSearchIterator.fwd.hh | |
| GridSearchIterator.hh | |
| GridSearchIteratorCA.cc | |
| GridSearchIteratorCA.fwd.hh | |
| GridSearchIteratorCA.hh | |
| PcsDataCenter.cc | |
| PcsDataCenter.fwd.hh | |
| PcsDataCenter.hh | Hold the PCS data on which the SVD will be applyed |
| PcsDataCenterManager.cc | |
| PcsDataCenterManager.fwd.hh | |
| PcsDataCenterManager.hh | |
| PcsDataCenterManagerSingleton.cc | |
| PcsDataCenterManagerSingleton.fwd.hh | |
| PcsDataCenterManagerSingleton.hh | |
| PcsDataLanthanide.cc | |
| PcsDataLanthanide.fwd.hh | |
| PcsDataLanthanide.hh | |
| PcsEnergy.cc | |
| PcsEnergy.fwd.hh | |
| PcsEnergy.hh | |
| PcsEnergyCreator.hh | Declaration for the class that connects PcsEnergyCreator with the ScoringManager |
| PcsEnergyParameter.cc | |
| PcsEnergyParameter.fwd.hh | |
| PcsEnergyParameter.hh | |
| PcsEnergyParameterManager.cc | |
| PcsEnergyParameterManager.fwd.hh | |
| PcsEnergyParameterManager.hh | |
| PcsGridSearchParameter.cc | |
| PcsGridSearchParameter.fwd.hh | |
| PcsGridSearchParameter.hh | |
| PcsGridSearchParameterManager.cc | |
| PcsGridSearchParameterManager.fwd.hh | |
| PcsGridSearchParameterManager.hh | |
| PcsInputCenter.cc | |
| PcsInputCenter.fwd.hh | Christophe Schmitz |
| PcsInputCenter.hh | This class hold the information for each paramagnetic center Multiple data set with different lanthanide can be measured for each paramagnetic center |
| PcsInputCenterManager.cc | Singleton that hold everything about the input PCS This avoid multiple reading of the input file |
| PcsInputCenterManager.fwd.hh | Christophe Schmitz |
| PcsInputCenterManager.hh | Singleton that hold everything about the input PCS This avoid multiple reading of the input files |
| PcsInputFile.cc | Read all input from a .npc input file, and hold the data in the class One file per lanthanide data |
| PcsInputFile.fwd.hh | Read all input from a .npc input file, and hold the data in the class |
| PcsInputFile.hh | Read all input from a .npc input file, and hold the data in the class. One file per lanthanide data |
| PcsInputLine.cc | |
| PcsInputLine.fwd.hh | Class that hold a line data of the input file |
| PcsInputLine.hh | Class that hold a line data of the input file |
| PcsTensor.cc | Hold chi-tensor information of PCS |
| PcsTensor.fwd.hh | |
| PcsTensor.hh | Hold chi-tensor information of PCS |
| TensorsOptimizer.cc | |
| TensorsOptimizer.fwd.hh | |
| TensorsOptimizer.hh | |
| TensorsOptimizerFix.cc | |
| TensorsOptimizerFix.fwd.hh | |
| TensorsOptimizerFix.hh | |
| TensorsOptimizerSvd.cc | |
| TensorsOptimizerSvd.fwd.hh | |
| TensorsOptimizerSvd.hh | |
| ► pcsTs1 | |
| GridSearchIterator.cc | |
| GridSearchIterator.fwd.hh | |
| GridSearchIterator.hh | |
| PseudocontactShiftData.cc | |
| PseudocontactShiftData.fwd.hh | |
| PseudocontactShiftData.hh | |
| PseudocontactShiftEnergy.cc | |
| PseudocontactShiftEnergy.fwd.hh | |
| PseudocontactShiftEnergy.hh | |
| PseudocontactShiftEnergyCreator.hh | |
| PseudocontactShiftInput.cc | |
| PseudocontactShiftInput.fwd.hh | |
| PseudocontactShiftInput.hh | |
| PseudocontactShiftTensor.cc | |
| PseudocontactShiftTensor.fwd.hh | |
| PseudocontactShiftTensor.hh | |
| TensorsOptimizer.cc | |
| TensorsOptimizer.fwd.hh | |
| TensorsOptimizer.hh | |
| ► pcsTs2 | |
| GridSearchIterator.cc | |
| GridSearchIterator.fwd.hh | |
| GridSearchIterator.hh | |
| PseudocontactShiftData.cc | |
| PseudocontactShiftData.fwd.hh | |
| PseudocontactShiftData.hh | |
| PseudocontactShiftEnergy.cc | |
| PseudocontactShiftEnergy.fwd.hh | |
| PseudocontactShiftEnergy.hh | |
| PseudocontactShiftEnergyCreator.hh | |
| PseudocontactShiftInput.cc | |
| PseudocontactShiftInput.fwd.hh | |
| PseudocontactShiftInput.hh | |
| PseudocontactShiftTensor.cc | |
| PseudocontactShiftTensor.fwd.hh | |
| PseudocontactShiftTensor.hh | |
| TensorsOptimizer.cc | |
| TensorsOptimizer.fwd.hh | |
| TensorsOptimizer.hh | |
| ► pcsTs3 | |
| GridSearchIterator.cc | |
| GridSearchIterator.fwd.hh | |
| GridSearchIterator.hh | |
| PseudocontactShiftData.cc | |
| PseudocontactShiftData.fwd.hh | |
| PseudocontactShiftData.hh | |
| PseudocontactShiftEnergy.cc | |
| PseudocontactShiftEnergy.fwd.hh | |
| PseudocontactShiftEnergy.hh | |
| PseudocontactShiftEnergyCreator.hh | |
| PseudocontactShiftInput.cc | |
| PseudocontactShiftInput.fwd.hh | |
| PseudocontactShiftInput.hh | |
| PseudocontactShiftTensor.cc | |
| PseudocontactShiftTensor.fwd.hh | |
| PseudocontactShiftTensor.hh | |
| TensorsOptimizer.cc | |
| TensorsOptimizer.fwd.hh | |
| TensorsOptimizer.hh | |
| ► pcsTs4 | |
| GridSearchIterator.cc | |
| GridSearchIterator.fwd.hh | |
| GridSearchIterator.hh | |
| PseudocontactShiftData.cc | |
| PseudocontactShiftData.fwd.hh | |
| PseudocontactShiftData.hh | |
| PseudocontactShiftEnergy.cc | |
| PseudocontactShiftEnergy.fwd.hh | |
| PseudocontactShiftEnergy.hh | |
| PseudocontactShiftEnergyCreator.hh | |
| PseudocontactShiftInput.cc | |
| PseudocontactShiftInput.fwd.hh | |
| PseudocontactShiftInput.hh | |
| PseudocontactShiftTensor.cc | |
| PseudocontactShiftTensor.fwd.hh | |
| PseudocontactShiftTensor.hh | |
| TensorsOptimizer.cc | |
| TensorsOptimizer.fwd.hh | |
| TensorsOptimizer.hh | |
| ► saxs | |
| PDDFEnergy.cc | |
| PDDFEnergy.fwd.hh | Forward declaration of a PDDF energy term |
| PDDFEnergy.hh | |
| PDDFEnergyCreator.hh | Declaration for the class that connects PDDFEnergyCreator with the ScoringManager |
| EnsembleEnergy.cc | Function to subtract out individual reference energies during ensemble docking |
| EnsembleEnergy.hh | |
| EnsembleEnergyCreator.hh | Declaration for the class that connects EnsembleEnergy with the ScoringManager |
| InterchainEnergy.fwd.hh | |
| InterchainEnvEnergy.cc | Statistically derived rotamer pair potentials |
| InterchainEnvEnergy.hh | |
| InterchainEnvEnergyCreator.hh | Declaration for the class that connects InterchainEnvEnergy with the ScoringManager |
| InterchainPairEnergy.cc | |
| InterchainPairEnergy.hh | |
| InterchainPairEnergyCreator.hh | |
| ResidualDipolarCouplingEnergyRigidSegments.cc | |
| ResidualDipolarCouplingEnergyRigidSegments.fwd.hh | |
| ResidualDipolarCouplingEnergyRigidSegments.hh | |
| ResidualDipolarCouplingEnergyRigidSegmentsCreator.hh | |
| SpecialRotamerEnergy.cc | |
| SpecialRotamerEnergy.fwd.hh | |
| SpecialRotamerEnergy.hh | Adds a bonus to any rotamer that is flagged |
| SpecialRotamerEnergyCreator.hh | Declaration for the class that connects SpecialRotamerEnergy with the ScoringManager |
| ImplicitFastClashCheck.cc | |
| ImplicitFastClashCheck.fwd.hh | |
| ImplicitFastClashCheck.hh | |
| InterchainPotential.cc | Statistically derived rotamer pair potentials |
| InterchainPotential.fwd.hh | |
| InterchainPotential.hh | |
| Interface.cc | |
| Interface.fwd.hh | |
| Interface.hh | |
| InterfaceInfo.cc | Statistically derived rotamer pair potentials |
| InterfaceInfo.fwd.hh | |
| InterfaceInfo.hh | |
| ResidualDipolarCouplingRigidSegments.cc | |
| ResidualDipolarCouplingRigidSegments.fwd.hh | |
| ResidualDipolarCouplingRigidSegments.hh | |
| ► seeded_abinitio | |
| CAcstGenerator.cc | |
| CAcstGenerator.hh | |
| CAcstGeneratorCreator.hh | |
| CloseFold.cc | |
| CloseFold.hh | |
| CloseFoldCreator.hh | |
| CoordinateCst.cc | Allows to add coordinate constraints to the pose based on parsed spans or residues residues specified are parsed at runtime not at parse time, so it can be used somewhat used with length changes currently it only adds CA constraints, but hopefully at some time point others too |
| CoordinateCst.hh | |
| CoordinateCstCreator.hh | |
| DefineMovableLoops.cc | |
| DefineMovableLoops.hh | |
| DefineMovableLoopsCreator.hh | |
| GrowPeptides.cc | Different ways of growing peptide sequences |
| GrowPeptides.hh | |
| GrowPeptidesCreator.hh | |
| PlaceFragments.cc | |
| PlaceFragments.hh | |
| PlaceFragmentsCreator.hh | |
| SeededAbinitio_util.cc | |
| SeededAbinitio_util.hh | |
| SeedFoldTree.cc | |
| SeedFoldTree.fwd.hh | |
| SeedFoldTree.hh | |
| SeedFoldTreeCreator.hh | |
| SeedSetupMover.cc | Mover to set up packer task and movemap for seededabinitio |
| SeedSetupMover.hh | |
| SeedSetupMoverCreator.hh | |
| SegmentHybridizer.cc | |
| SegmentHybridizer.hh | Repurposing logic and some functions from CartesianHybridze protocols for segment insertions and chain closure |
| SegmentHybridizerCreator.hh | |
| SwapSegment.cc | |
| SwapSegment.hh | |
| SwapSegmentCreator.hh | |
| util.cc | |
| util.hh | |
| ► sic_dock | |
| ► scores | |
| MotifHashRigidScore.cc | |
| MotifHashRigidScore.fwd.hh | |
| MotifHashRigidScore.hh | |
| TrisBpyScore.cc | |
| TrisBpyScore.fwd.hh | |
| TrisBpyScore.hh | |
| designability_score.cc | |
| designability_score.hh | |
| loophash_util.cc | |
| loophash_util.hh | |
| read_biounit.cc | |
| read_biounit.hh | |
| RigidScore.cc | |
| RigidScore.fwd.hh | |
| RigidScore.hh | |
| Rose.cc | |
| Rose.fwd.hh | |
| Rose.hh | |
| SICFast.cc | |
| SICFast.fwd.hh | |
| SICFast.hh | |
| types.hh | |
| util.cc | |
| util.hh | |
| xyzStripeHashPose.cc | |
| xyzStripeHashPose.fwd.hh | |
| xyzStripeHashPose.hh | |
| xyzStripeHashPoseWithMeta.fwd.hh | |
| xyzStripeHashPoseWithMeta.hh | |
| ► simple_filters | |
| AbinitioBaseFilter.cc | |
| AbinitioBaseFilter.hh | Header file for AbinitioBaseFilter.cc |
| AlaScan.cc | |
| AlaScan.fwd.hh | |
| AlaScan.hh | Definition of filter class AlsScan |
| AlaScanCreator.hh | FilterCreators for the AlaScanCreator |
| AtomicContactFilter.cc | |
| AtomicContactFilter.hh | |
| AtomicContactFilterCreator.hh | FilterCreator for the AtomicContactFilter |
| AtomicDistanceFilter.cc | |
| AtomicDistanceFilter.hh | Filter for looking at specific atom distances |
| AtomicDistanceFilterCreator.hh | FilterCreator for the AtomicDistanceFilter |
| AveragePathLengthFilter.cc | Filter on the average covalent path length between residues, including disulfides |
| AveragePathLengthFilter.fwd.hh | Filter on the average covalent path length between residues, including disulfides |
| AveragePathLengthFilter.hh | Filter on the average covalent path length between residues, including disulfides |
| AveragePathLengthFilterCreator.hh | FilterCreators for the AveragePathLengthFilter |
| BatchNrEvaluator.cc | |
| BatchNrEvaluator.hh | |
| BuriedRegionsFilter.cc | Implementation of BuriedRegionsFilter which checks whether a defined region of a protein is buried in an interface by evaluating the number of non-water neighbors of each residue |
| BuriedRegionsFilter.fwd.hh | Forward declaration for BuriedRegionsFilter which checks if a query region is buried in an interface by evaluating the number of non-water neighbors of each residue |
| BuriedRegionsFilter.hh | Header file for BuriedRegionsFilter which checks whether a defined region of a protein is buried in an interface by evaluating the number of non-water neighbors of all residues |
| BuriedUnsatHbondFilter.cc | |
| BuriedUnsatHbondFilter.fwd.hh | |
| BuriedUnsatHbondFilter.hh | Definition of filter class BuriedUnsatHbondFilter |
| BuriedUnsatHbondFilterCreator.hh | FilterCreators for the BuriedUnsatHbondFilterCreator |
| CamShiftEvaluator.cc | |
| CamShiftEvaluator.hh | |
| CamShiftEvaluatorCreator.cc | |
| CamShiftEvaluatorCreator.hh | Header for CamShiftEvaluatorCreator |
| ChiWellRmsdEvaluator.cc | |
| ChiWellRmsdEvaluator.hh | |
| ChiWellRmsdEvaluatorCreator.cc | |
| ChiWellRmsdEvaluatorCreator.hh | Header for ChiWellRmsdEvaluatorCreator |
| ClashEvaluator.cc | |
| ClashEvaluator.hh | |
| COFilter.cc | Runs reject or accept filters on pose |
| COFilter.hh | |
| ConservedPosMutationFilter.cc | |
| ConservedPosMutationFilter.fwd.hh | |
| ConservedPosMutationFilter.hh | Header file for ConservedPosMutationFitler class |
| ConservedPosMutationFilterCreator.hh | FilterCreator for the ConservedPosMutationFilter |
| ConstraintScoreCutoffFilter.cc | |
| ConstraintScoreCutoffFilter.fwd.hh | |
| ConstraintScoreCutoffFilter.hh | Header file for ConstraintScoreCutoffFitler class |
| ConstraintScoreCutoffFilterCreator.hh | FilterCreator for the ConstraintScoreCutoffFilter |
| ContactMapEvaluator.cc | |
| ContactMapEvaluator.hh | |
| ContactMapEvaluatorCreator.cc | |
| ContactMapEvaluatorCreator.hh | Header for ContactMapEvaluatorCreator |
| DdgFilter.cc | |
| DdgFilter.fwd.hh | |
| DdgFilter.hh | Definition of filter class DdgFilter |
| DdgFilterCreator.hh | FilterCreators for the DdgFilterCreator |
| DeltaFilter.cc | |
| DeltaFilter.fwd.hh | Forward declaration for DeltaFilter |
| DeltaFilter.hh | Reports the average degree of connectivity of interface residues |
| DeltaFilterCreator.hh | FilterCreators for the DeltaFilter |
| DisulfideEntropyFilter.cc | Filter on the entropic effect of disulfide linkage |
| DisulfideEntropyFilter.fwd.hh | Filter on the entropic effect of disulfide linkage |
| DisulfideEntropyFilter.hh | Filter on the entropic effect of disulfide linkage |
| DisulfideEntropyFilterCreator.hh | FilterCreators for the DisulfideEntropyFilter |
| DomainInterfaceFilter.cc | Implementation of DomainInterfaceFilter which checks whether a defined region of a protein is part of an interface with a pre-defined other domain of the protein |
| DomainInterfaceFilter.fwd.hh | Forward declaration for DomainInterfaceFilter which checks if a query region is part of an an interface with a pre-defined other domain of a protein |
| DomainInterfaceFilter.hh | Header file for DomainInterfaceFilter which checks whether a defined region of a protein is buried in an interface by evaluating the number of non-water neighbors of all residues |
| EnergyPerResidueFilter.cc | |
| EnergyPerResidueFilter.fwd.hh | |
| EnergyPerResidueFilter.hh | Definition of filter class EnergyPerResidueFilter |
| EnergyPerResidueFilterCreator.hh | FilterCreators for the EnergyPerResidueFilterCreator |
| EvaluatedTrialMover.cc | |
| EvaluatedTrialMover.hh | |
| ExpiryFilter.cc | |
| ExpiryFilter.fwd.hh | |
| ExpiryFilter.hh | Simple filter that tests whether a file exists. Useful to test whether we're recovering from a checkpoint |
| ExpiryFilterCreator.hh | FilterCreators for the ExpiryFilter |
| ExternalEvaluator.cc | |
| ExternalEvaluator.hh | |
| ExtraScoreEvaluatorCreator.cc | |
| ExtraScoreEvaluatorCreator.hh | Header for ExtraScoreEvaluatorCreator |
| FileExistFilter.cc | |
| FileExistFilter.fwd.hh | |
| FileExistFilter.hh | Simple filter that tests whether a file exists. Useful to test whether we're recovering from a checkpoint |
| FileExistFilterCreator.hh | FilterCreators for the FileExistFilter |
| FileRemoveFilter.cc | |
| FileRemoveFilter.fwd.hh | |
| FileRemoveFilter.hh | Simple filter that tests whether a file exists. Useful to test whether we're recovering from a checkpoint |
| FileRemoveFilterCreator.hh | FilterCreators for the FileRemoveFilter |
| GeometryFilter.cc | |
| GeometryFilter.fwd.hh | |
| GeometryFilter.hh | Definition of filter class GeometryFilter |
| GeometryFilterCreator.hh | FilterCreators for the GeometryFilterCreator |
| HolesFilter.cc | |
| HolesFilter.fwd.hh | Filter structures by will's hole score |
| HolesFilter.hh | Header file for HolesFilter class |
| HolesFilterCreator.hh | FilterCreator for the HolesFilter |
| InterfaceBindingEnergyDensityFilter.cc | Implementation of the binding-energy-density filter |
| InterfaceBindingEnergyDensityFilter.fwd.hh | Forward declaration and typedefs for InterfaceBindingEnergyDensityFilter |
| InterfaceBindingEnergyDensityFilter.hh | Filter class for looking at the dGbind/dSASA ratio |
| InterfaceBindingEnergyDensityFilterCreator.hh | FilterCreators for the InterfaceBindingEnergyDensityFilterCreator |
| InterfaceSasaFilter.cc | |
| InterfaceSasaFilter.fwd.hh | |
| InterfaceSasaFilter.hh | Definition of filter class InterfaceSasaFilter |
| InterfaceSasaFilterCreator.hh | FilterCreators for the InterfaceSasaFilterCreator |
| JScoreEvaluator.cc | |
| JScoreEvaluator.hh | |
| JScoreEvaluatorCreator.cc | |
| JScoreEvaluatorCreator.hh | Header for JScoreEvaluatorCreator |
| JumpEvaluator.cc | |
| JumpEvaluator.hh | |
| JumpNrEvaluatorCreator.cc | |
| JumpNrEvaluatorCreator.hh | Header for JumpNrEvaluatorCreator |
| MinValueEvaluator.hh | |
| MultipleSigmoidsFilter.cc | |
| MultipleSigmoidsFilter.fwd.hh | |
| MultipleSigmoidsFilter.hh | |
| MultipleSigmoidsFilterCreator.hh | FilterCreators for the MultipleSigmoidsFilter |
| NativeEvaluatorCreator.cc | |
| NativeEvaluatorCreator.hh | Header for NativeEvaluatorCreator |
| NeighborTypeFilter.cc | |
| NeighborTypeFilter.fwd.hh | |
| NeighborTypeFilter.hh | Definition of filter class InterfaceSasaFilter |
| NeighborTypeFilterCreator.hh | FilterCreators for the NeighborTypeFilterCreator |
| NetChargeFilter.cc | |
| NetChargeFilter.fwd.hh | |
| NetChargeFilter.hh | Definition of filter class NetChargeFilter |
| NetChargeFilterCreator.hh | FilterCreators for the NetChargeFilterCreator |
| NMerPSSMEnergyFilter.cc | |
| NMerPSSMEnergyFilter.fwd.hh | |
| NMerPSSMEnergyFilter.hh | Definition of filter class NMerPSSMEnergyFilter |
| NMerPSSMEnergyFilterCreator.hh | FilterCreators for the NMerPSSMEnergyFilter |
| NMerSVMEnergyFilter.cc | |
| NMerSVMEnergyFilter.fwd.hh | |
| NMerSVMEnergyFilter.hh | Definition of filter class NMerSVMEnergyFilter |
| NMerSVMEnergyFilterCreator.hh | FilterCreators for the NMerSVMEnergyFilter |
| NonSequentialNeighborsFilter.cc | |
| NonSequentialNeighborsFilter.fwd.hh | |
| NonSequentialNeighborsFilter.hh | Simple filter that tests whether a file exists. Useful to test whether we're recovering from a checkpoint |
| NonSequentialNeighborsFilterCreator.hh | FilterCreators for the NonSequentialNeighborsFilter |
| OperatorFilter.cc | |
| OperatorFilter.fwd.hh | |
| OperatorFilter.hh | |
| OperatorFilterCreator.hh | FilterCreators for the OperatorFilter |
| PackerNeighborGraphFilter.cc | |
| PackerNeighborGraphFilter.hh | Header file for packer neighbor graph based filter |
| PackStatFilter.cc | |
| PackStatFilter.fwd.hh | |
| PackStatFilter.hh | Header file for PackStatFilter class |
| PackStatFilterCreator.hh | FilterCreator for the PackStatFilter |
| PalesEvaluator.cc | |
| PalesEvaluator.hh | |
| PalesEvaluatorCreator.cc | |
| PalesEvaluatorCreator.hh | Header for PalesEvaluatorCreator |
| PDDFScoreFilter.cc | Runs reject or accept filters on pose |
| PDDFScoreFilter.fwd.hh | |
| PDDFScoreFilter.hh | |
| PoolEvaluatorCreator.cc | |
| PoolEvaluatorCreator.hh | Header for PoolEvaluatorCreator |
| PoseCommentFilter.cc | |
| PoseCommentFilter.fwd.hh | |
| PoseCommentFilter.hh | |
| PoseCommentFilterCreator.hh | FilterCreators for the PoseCommentFilter |
| PoseInfoFilter.cc | |
| PoseInfoFilter.hh | Filter for outputing information about the pose |
| PoseInfoFilterCreator.hh | FilterCreator for the PoseInfoFilter |
| PoseMetricEvaluator.hh | |
| PredictedBurialEvaluator.cc | |
| PredictedBurialEvaluator.hh | |
| PredictedBurialFnEvaluatorCreator.cc | |
| PredictedBurialFnEvaluatorCreator.hh | Header for PredictedBurialFnEvaluatorCreator |
| RangeFilter.cc | |
| RangeFilter.fwd.hh | |
| RangeFilter.hh | Range filter evaluates if the return value of a particular filter is between a specific range |
| RangeFilterCreator.hh | FilterCreator for the RangeFilter |
| RDC_Evaluator.cc | |
| RDC_Evaluator.fwd.hh | |
| RDC_Evaluator.hh | |
| RdcEvaluatorCreator.cc | |
| RdcEvaluatorCreator.hh | Header for RdcEvaluatorCreator |
| RdcSelectEvaluatorCreator.cc | |
| RdcSelectEvaluatorCreator.hh | Header for RdcSelectEvaluatorCreator |
| RdcTargetEvaluatorCreator.cc | |
| RdcTargetEvaluatorCreator.hh | Header for RdcTargetEvaluatorCreator |
| RelativePoseFilter.cc | |
| RelativePoseFilter.fwd.hh | |
| RelativePoseFilter.hh | Computes a filter's value on a pose that is modified from one that is read from disk. Useful for computing values for the same sequence across many structures |
| RelativePoseFilterCreator.hh | |
| ReportFilter.cc | |
| ReportFilter.fwd.hh | |
| ReportFilter.hh | Simple filter that tests whether a file exists. Useful to test whether we're recovering from a checkpoint |
| ReportFilterCreator.hh | FilterCreators for the ReportFilter |
| ResidueBurialFilter.cc | |
| ResidueBurialFilter.fwd.hh | |
| ResidueBurialFilter.hh | Definition of filter class ResidueBurialFilter |
| ResidueBurialFilterCreator.hh | FilterCreator for the ResidueBurialFilter |
| ResidueCountFilter.cc | Filter on the total number of residues in the structure |
| ResidueCountFilter.fwd.hh | Filter on the total number of residues in the structure |
| ResidueCountFilter.hh | Filter on the total number of residues in the structure |
| ResidueCountFilterCreator.hh | FilterCreators for the ResidueCountFilter |
| ResidueDistanceFilter.cc | |
| ResidueDistanceFilter.fwd.hh | |
| ResidueDistanceFilter.hh | Definition of filter class ResidueDistanceFilter |
| ResidueDistanceFilterCreator.hh | FilterCreator for the ResidueDistanceFilter |
| ResidueIEFilter.cc | |
| ResidueIEFilter.fwd.hh | |
| ResidueIEFilter.hh | Definition of filter class ResidueIEFilter |
| ResidueIEFilterCreator.hh | FilterCreators for the ResidueIEFilterCreator |
| ResidueSetChainEnergyFilter.cc | |
| ResidueSetChainEnergyFilter.fwd.hh | |
| ResidueSetChainEnergyFilter.hh | Definition of filter class ResidueSetChainEnergyFilter |
| ResidueSetChainEnergyFilterCreator.hh | FilterCreators for the ResidueSetChainEnergyFilter |
| ResiduesInInterfaceFilter.cc | |
| ResiduesInInterfaceFilter.fwd.hh | |
| ResiduesInInterfaceFilter.hh | Reports to Tracer which residues are designable in a taskfactory |
| ResiduesInInterfaceFilterCreator.hh | FilterCreators for the ResiduesInInterfaceFilter |
| RGFilter.cc | Runs reject or accept filters on pose |
| RGFilter.hh | |
| RGFilterCreator.hh | FilterCreator for the RGFilter |
| RmsdEvaluator.cc | |
| RmsdEvaluator.hh | |
| RmsdEvaluatorCreator.cc | |
| RmsdEvaluatorCreator.hh | Header for RmsdEvaluatorCreator |
| RmsdTargetEvaluatorCreator.cc | |
| RmsdTargetEvaluatorCreator.hh | Header for RmsdTargetEvaluatorCreator |
| RotamerBoltzmannWeight.cc | |
| RotamerBoltzmannWeight.fwd.hh | |
| RotamerBoltzmannWeight.hh | Reports to Tracer which residues are designable in a taskfactory |
| RotamerBoltzmannWeightFilterCreator.hh | FilterCreators for the RotamerBoltzmannWeightFilter |
| RPF_ScoreEvaluator.cc | |
| RPF_ScoreEvaluator.hh | |
| SavePoseConstraintToFileFilter.cc | |
| SavePoseConstraintToFileFilter.hh | Filter for outputing information about the pose |
| SavePoseConstraintToFileFilterCreator.hh | FilterCreator for the SavePoseConstraintToFileFilter |
| SAXSScoreFilter.cc | Runs reject or accept filters on pose |
| SAXSScoreFilter.fwd.hh | |
| SAXSScoreFilter.hh | |
| ScoreCutoffFilter.cc | |
| ScoreCutoffFilter.fwd.hh | |
| ScoreCutoffFilter.hh | Header file for ScoreCutoffFitler class |
| ScoreCutoffFilterCreator.hh | FilterCreator for the ScoreCutoffFilter |
| ScoreEvaluator.cc | |
| ScoreEvaluator.hh | |
| ScoreTypeFilter.cc | |
| ScoreTypeFilter.fwd.hh | |
| ScoreTypeFilter.hh | Definition of filter class ScoreTypeFilter |
| ScoreTypeFilterCreator.hh | FilterCreators for the ScoreTypeFilter |
| ShapeComplementarityFilter.cc | |
| ShapeComplementarityFilter.fwd.hh | |
| ShapeComplementarityFilter.hh | Header file for ShapeComplementarityFilter class |
| ShapeComplementarityFilterCreator.hh | FilterCreator for the ShapeComplementarityFilter |
| SheetFilter.cc | Runs reject or accept filters on pose |
| SheetFilter.hh | |
| SidechainRmsdFilter.cc | A filter based on automorphic sidechain RMSD |
| SidechainRmsdFilter.fwd.hh | A filter based on automorphic sidechain RMSD |
| SidechainRmsdFilter.hh | A filter based on automorphic sidechain RMSD |
| SidechainRmsdFilterCreator.hh | |
| SigmoidFilter.cc | |
| SigmoidFilter.fwd.hh | |
| SigmoidFilter.hh | |
| SigmoidFilterCreator.hh | FilterCreators for the SigmoidFilter |
| StructuralSimilarityEvaluator.cc | |
| StructuralSimilarityEvaluator.fwd.hh | Forward declaration for StructuralSimilarityEvaluator class |
| StructuralSimilarityEvaluator.hh | |
| StructureSimilarityEvaluatorCreator.cc | |
| StructureSimilarityEvaluatorCreator.hh | Header for StructureSimilarityEvaluatorCreator |
| SymmetricMotifFilter.cc | |
| SymmetricMotifFilter.hh | |
| SymmetricMotifFilterCreator.hh | |
| TerminusDistanceFilter.cc | |
| TerminusDistanceFilter.fwd.hh | |
| TerminusDistanceFilter.hh | Definition of filter class TerminusDistanceFilter |
| TerminusDistanceFilterCreator.hh | FilterCreators for the TerminusDistanceFilterCreator |
| TotalSasaFilter.cc | |
| TotalSasaFilter.fwd.hh | |
| TotalSasaFilter.hh | Definition of filter class TotalSasaFilter |
| TotalSasaFilterCreator.hh | FilterCreators for the TotalSasaFilterCreator |
| ► simple_moves | |
| ► asym_fold_and_dock | |
| AsymFoldandDockMoveRbJumpMover.cc | |
| AsymFoldandDockMoveRbJumpMover.fwd.hh | |
| AsymFoldandDockMoveRbJumpMover.hh | |
| AsymFoldandDockRbTrialMover.cc | |
| AsymFoldandDockRbTrialMover.fwd.hh | |
| AsymFoldandDockRbTrialMover.hh | |
| ► chiral | |
| ChiralMover.cc | ChiralMover methods implemented |
| ChiralMover.fwd.hh | ChiralMover forward declarations header |
| ChiralMover.hh | |
| ► hbs | |
| HbsMover.cc | HbsMover methods implemented |
| HbsMover.fwd.hh | HbsMover forward declarations header |
| HbsMover.hh | |
| HbsPatcher.cc | HbsPatcher methods implemented |
| HbsPatcher.fwd.hh | HbsPatcher forward declarations header |
| HbsPatcher.hh | |
| HbsRandomSmallMover.cc | HbsRandomSmallMover methods implemented |
| HbsRandomSmallMover.fwd.hh | HbsRandomSmallMover forward declarations header |
| HbsRandomSmallMover.hh | |
| ► oop | |
| OopMover.cc | OopMover methods implemented |
| OopMover.fwd.hh | OopMover forward declarations header |
| OopMover.hh | |
| OopPatcher.cc | OopPatcher methods implemented |
| OopPatcher.fwd.hh | OopPatcher forward declarations header |
| OopPatcher.hh | |
| OopPuckMover.cc | OopPuckMover methods implemented |
| OopPuckMover.fwd.hh | OopPuckMover forward declarations header |
| OopPuckMover.hh | |
| OopRandomPuckMover.cc | OopRandomPuckMover methods implemented |
| OopRandomPuckMover.fwd.hh | OopRandomPuckMover forward declarations header |
| OopRandomPuckMover.hh | |
| OopRandomSmallMover.cc | OopRandomSmallMover methods implemented |
| OopRandomSmallMover.fwd.hh | OopRandomSmallMover forward declarations header |
| OopRandomSmallMover.hh | |
| ► rational_mc | |
| RationalMonteCarlo.cc | |
| RationalMonteCarlo.fwd.hh | |
| RationalMonteCarlo.hh | |
| ► sidechain_moves | |
| JumpRotamerSidechainMover.cc | |
| JumpRotamerSidechainMover.fwd.hh | |
| JumpRotamerSidechainMover.hh | Definition of JumpRotamerSidechainMover class and functions |
| JumpRotamerSidechainMoverCreator.hh | This class will create instances of protocols::moves::Mover JumpRotamerSidechainMover for the protocols::moves::MoverFactory |
| PerturbChiSidechainMover.cc | |
| PerturbChiSidechainMover.fwd.hh | |
| PerturbChiSidechainMover.hh | Definition of PerturbChiSidechainMover class and functions |
| PerturbChiSidechainMoverCreator.hh | This class will create instances of protocols::moves::Mover PerturbChiSidechainMover for the protocols::moves::MoverFactory |
| PerturbRotamerSidechainMover.cc | |
| PerturbRotamerSidechainMover.fwd.hh | |
| PerturbRotamerSidechainMover.hh | Definition of PerturbRotamerSidechainMover class and functions |
| PerturbRotamerSidechainMoverCreator.hh | This class will create instances of protocols::moves::Mover PerturbRotamerSidechainMover for the protocols::moves::MoverFactory |
| SetChiMover.cc | A mover to change one chi angle |
| SetChiMover.fwd.hh | A mover to change one chi angle |
| SetChiMover.hh | A mover to change one chi angle |
| SetChiMoverCreator.hh | A mover to change one chi angle |
| SidechainMCMover.cc | Implementation of SidechainMCMover class and functions |
| SidechainMCMover.fwd.hh | |
| SidechainMCMover.hh | Definition of SidechainMCMover class and functions |
| SidechainMCMoverCreator.hh | This class will create instances of protocols::moves::Mover SidechainMCMover for the protocols::moves::MoverFactory |
| SidechainMover.cc | Implementation of SidechainMover class and functions |
| SidechainMover.fwd.hh | |
| SidechainMover.hh | Definition of SidechainMover class and functions |
| SidechainMoverBase.cc | Implementation of JumpRotamerSidechainMover class and functions |
| SidechainMoverBase.fwd.hh | |
| SidechainMoverBase.hh | Definition of SidechainMoverBase class and functions |
| SidechainMoverCreator.hh | This class will create instances of protocols::moves::Mover SidechainMover for the protocols::moves::MoverFactory |
| ► symmetry | |
| DetectSymmetryMover.cc | Automatical detection and setup of the symmetry machinery from an assymetric pose made of symmetric chains. Only works with cyclic simmetries |
| DetectSymmetryMover.fwd.hh | |
| DetectSymmetryMover.hh | Automatical detection and setup of the symmetry machinery from an asymetric pose made of symmetric chains. Only works with cyclic simmetries |
| DetectSymmetryMoverCreator.hh | |
| SetupForSymmetryMover.cc | |
| SetupForSymmetryMover.fwd.hh | |
| SetupForSymmetryMover.hh | |
| SetupForSymmetryMoverCreator.hh | |
| SetupNCSMover.cc | Sets up NCS restraints |
| SetupNCSMover.fwd.hh | Sets up NCS restraints |
| SetupNCSMover.hh | Sets up NCS restraints |
| SetupNCSMoverCreator.hh | Protocols::moves::MoverCreator for SetupNCSMover |
| SymDockingInitialPerturbation.cc | |
| SymDockingInitialPerturbation.hh | |
| SymmetricRMSMover.cc | |
| SymmetricRMSMover.fwd.hh | |
| SymmetricRMSMover.hh | |
| SymMinMover.cc | |
| SymMinMover.fwd.hh | MinMover forward declarations header |
| SymMinMover.hh | |
| SymMinMoverCreator.hh | |
| SymPackRotamersMover.cc | |
| SymPackRotamersMover.fwd.hh | |
| SymPackRotamersMover.hh | |
| SymPackRotamersMoverCreator.hh | |
| SymRotamerTrialsMover.cc | |
| SymRotamerTrialsMover.fwd.hh | |
| SymRotamerTrialsMover.hh | |
| SymRotamerTrialsMoverCreator.hh | |
| SymShakeStructureMover.cc | |
| SymShakeStructureMover.fwd.hh | |
| SymShakeStructureMover.hh | |
| AddCavitiesMover.cc | |
| AddCavitiesMover.hh | |
| AddChainMover.cc | |
| AddChainMover.fwd.hh | Add chain to an existing pose (as a new chain) |
| AddChainMover.hh | Switch the chain order |
| AddChainMoverCreator.hh | |
| AddConstraintsToCurrentConformationMover.cc | Add constraints to the current pose conformation |
| AddConstraintsToCurrentConformationMover.hh | Add constraints to the current pose conformation |
| AddConstraintsToCurrentConformationMoverCreator.hh | |
| AddJobPairData.cc | A really simple mover that takes some data in through xml and appends it to the pose |
| AddJobPairData.fwd.hh | Forward Header file for the AddJobPairData Mover |
| AddJobPairData.hh | Header file for the AddJobPairData Mover |
| AddJobPairDataCreator.hh | MoverCreator definitions for the AddJobPairData mover |
| AlignChainMover.cc | |
| AlignChainMover.fwd.hh | |
| AlignChainMover.hh | Switch the chain order |
| AlignChainMoverCreator.hh | |
| BackboneMover.cc | Method definitions for SmallMover and ShearMover |
| BackboneMover.fwd.hh | BackboneMover forward declarations header |
| BackboneMover.hh | Declarations and simple accessor/mutator definitions for SmallMover and ShearMover |
| BackboneMoverCreator.hh | This class will create instances of protocols::moves::Movers SmallMover and ShearMover for the protocols::moves::MoverFactory |
| BBConRotMover.cc | |
| BBConRotMover.fwd.hh | |
| BBConRotMover.hh | |
| BBGaussianMover.cc | |
| BBGaussianMover.fwd.hh | -*- mode:c++;tab-width:2;indent-tabs-mode:t;show-trailing-whitespace:t;rm-trailing-spaces:t -*- |
| BBGaussianMover.hh | |
| BBGaussianMoverCreator.hh | |
| ChainSplitMover.cc | |
| ChainSplitMover.fwd.hh | Forward declaration of ChainSplitMover which splits a pose into two chains at a given cutpoint |
| ChainSplitMover.hh | Declaration of ChainSplitMover which splits a pose into two chains at a given cutpoint |
| ClearConstraintsMover.cc | Add constraints to the current pose conformation |
| ClearConstraintsMover.hh | Add constraints to the current pose conformation |
| ClearConstraintsMoverCreator.hh | |
| ConsensusDesignMover.cc | Cc file for ConsensusDesignMover |
| ConsensusDesignMover.fwd.hh | Fwd.hh file for ConsensusDesignMover |
| ConsensusDesignMover.hh | Header file for ConsensusDesignMover |
| ConsensusDesignMoverCreator.hh | |
| ConstraintFragmentMover.hh | |
| ConstrainToIdealMover.cc | Adds to your pose constraints suitable for idealization of bond lengths and angles |
| ConstrainToIdealMover.fwd.hh | ConstrainToIdealMover forward declarations header |
| ConstrainToIdealMover.hh | Adds to your pose constraints suitable for idealization of bond lengths and angles |
| ConstraintSetMover.cc | Assigns a ConstraintSet to a pose. Reads and creats ConstraintSet from file via command line option -constraintscst_file, unless a ConstraintSet is supplied via the constructor or the constraint_set() method |
| ConstraintSetMover.fwd.hh | |
| ConstraintSetMover.hh | Assigns a ConstraintSet to a pose. Reads and creats ConstraintSet from file via command line option -constraintscst_file, unless a ConstraintSet is supplied via the constructor or the constraint_set() method |
| ConstraintSetMoverCreator.hh | |
| ContingentAcceptMover.cc | |
| ContingentAcceptMover.fwd.hh | Switch the chain order |
| ContingentAcceptMover.hh | Switch the chain order |
| ContingentAcceptMoverCreator.hh | |
| CopyDofMover.cc | |
| CopyDofMover.fwd.hh | |
| CopyDofMover.hh | |
| CutChainMover.cc | |
| CutChainMover.fwd.hh | |
| CutChainMover.hh | |
| CutChainMoverCreator.hh | |
| ddG.cc | Implementation of the ddG class for computing interface delta dGs |
| ddG.fwd.hh | Forward declarations for ddG |
| ddG.hh | |
| ddGCreator.hh | |
| DesignRepackMover.cc | |
| DesignRepackMover.fwd.hh | Forward declations for DesignRepackMover |
| DesignRepackMover.hh | |
| DME_FilterMover.cc | |
| DME_FilterMover.hh | |
| DOFHistogramRecorder.cc | |
| DOFHistogramRecorder.fwd.hh | Forward declarations for class DOFHistogramRecorder |
| DOFHistogramRecorder.hh | |
| DumpPdb.cc | |
| DumpPdb.hh | |
| DumpPdbCreator.hh | |
| ExtendedPoseMover.cc | |
| ExtendedPoseMover.fwd.hh | |
| ExtendedPoseMover.hh | |
| ExtendedPoseMoverCreator.cc | |
| ExtendedPoseMoverCreator.hh | |
| FavorSequenceProfile.cc | Add a SequenceProfileConstraint to a pose |
| FavorSequenceProfile.hh | Add a SequenceProfileConstraint to a pose |
| FavorSequenceProfileCreator.hh | Declaration of the protocols::moves::MoverCreator class for the FavorSequenceProfile |
| FavorSymmetricSequence.cc | Apply constraints to enforce a symmetric sequence |
| FavorSymmetricSequence.fwd.hh | Apply constraints to enforce a symmetric sequence |
| FavorSymmetricSequence.hh | Apply constraints to enforce a symmetric sequence |
| FavorSymmetricSequenceCreator.hh | Apply constraints to enforce a symmetric sequence |
| ForceDisulfidesMover.cc | |
| ForceDisulfidesMover.fwd.hh | ForceDisulfidesMover forward declarations header |
| ForceDisulfidesMover.hh | |
| ForceDisulfidesMoverCreator.hh | |
| FragmentMover.cc | |
| FragmentMover.fwd.hh | |
| FragmentMover.hh | |
| GenericMonteCarloMover.cc | |
| GenericMonteCarloMover.fwd.hh | |
| GenericMonteCarloMover.hh | Perform a given mover and sample structures by MonteCarlo |
| GenericMonteCarloMoverCreator.hh | |
| GreenPacker.cc | Packing mover that makes extensive reuse of rotamer pair energies class definition |
| GreenPacker.fwd.hh | Packing mover that makes extensive reuse of rotamer pair energies class forward declaration |
| GreenPacker.hh | Packing mover that makes extensive reuse of rotamer pair energies class declaration |
| GunnCost.cc | |
| GunnCost.hh | |
| HelicalPeptideLengthMover.cc | Appends or prepends a single residue to a helical peptide that's attached to the rest of the pose by a jump |
| HelicalPeptideLengthMover.fwd.hh | |
| HelicalPeptideLengthMover.hh | Definition of classes for changing the length of a helical peptide that's connected to the rest of the pose by a jump |
| LoadPDBMover.cc | Simple mover that loads a pdb from file and replaces the current pdb with it. Useful for checkpointing |
| LoadPDBMover.fwd.hh | Switch the chain order |
| LoadPDBMover.hh | Switch the chain order |
| LoadPDBMoverCreator.hh | |
| LoadUnboundRotMover.cc | LoadUnboundRotMover methods implemented |
| LoadUnboundRotMover.fwd.hh | |
| LoadUnboundRotMover.hh | |
| LoadUnboundRotMoverCreator.hh | |
| MakePolyXMover.cc | Convert pose to poly XXX: any amino acid, default poly Ala |
| MakePolyXMover.fwd.hh | Convert pose to poly XXX: any amino acid, default poly Ala |
| MakePolyXMover.hh | Header file of MakePolyXMover.cc |
| MakePolyXMoverCreator.hh | This class will create instances of protocols::moves::Mover MakePolyXMover for the protocols::moves::MoverFactory |
| MembraneTopology.cc | |
| MembraneTopology.fwd.hh | |
| MembraneTopology.hh | |
| MembraneTopologyCreator.hh | |
| MinMover.cc | |
| MinMover.fwd.hh | MinMover forward declarations header |
| MinMover.hh | |
| MinMoverCreator.hh | |
| MinPackMover.cc | Implementation of the MinPackMover class; a wrapper class for invoking core::pack::min_pack |
| MinPackMover.fwd.hh | Forward declaration of the mover class to both pack and minimize rotamers |
| MinPackMover.hh | Protocols::moves::Mover class to invoke core::pack::min_pack |
| MinPackMoverCreator.hh | This class will create instances of protocols::moves::Mover MinPackMover for the protocols::moves::MoverFactory |
| MissingDensityToJumpMover.cc | Implementation of mover that inserts a jump where there is gap in the pdb. This gap corresponds to missing density |
| MissingDensityToJumpMover.fwd.hh | Implementation of mover that inserts a jump where there is gap in the pdb. This gap corresponds to missing density |
| MissingDensityToJumpMover.hh | |
| ModifyVariantTypeMover.cc | Modify variant type to residues |
| ModifyVariantTypeMover.fwd.hh | |
| ModifyVariantTypeMover.hh | |
| ModifyVariantTypeMoverCreator.hh | |
| MonteCarloRecover.cc | |
| MonteCarloRecover.fwd.hh | |
| MonteCarloRecover.hh | |
| MonteCarloRecoverCreator.hh | |
| MonteCarloReset.cc | |
| MonteCarloReset.fwd.hh | |
| MonteCarloReset.hh | Perform a given mover and sample structures by MonteCarlo |
| MonteCarloResetCreator.hh | |
| MonteCarloTest.cc | |
| MonteCarloTest.fwd.hh | |
| MonteCarloTest.hh | Perform a given mover and sample structures by MonteCarlo |
| MonteCarloTestCreator.hh | |
| MutateResidue.cc | |
| MutateResidue.fwd.hh | |
| MutateResidue.hh | |
| MutateResidueCreator.hh | |
| O2M_MutateMover.cc | Mover that takes a single starting structure and some task ops, and produces every single possible point mutation DOES NOT WORK WITH ROSETTASCRIPTS |
| O2M_MutateMover.fwd.hh | O2M_MutateMover forward declarations header |
| O2M_MutateMover.hh | Mover that takes a starting structure and some task ops, and produces every single possible point mutation DOES NOT WORK WITH ROSETTASCRIPTS |
| PackRotamersMover.cc | |
| PackRotamersMover.fwd.hh | |
| PackRotamersMover.hh | |
| PackRotamersMoverCreator.hh | |
| PackRotamersMoverLazy.cc | |
| PackRotamersMoverLazy.fwd.hh | |
| PackRotamersMoverLazy.hh | |
| PackRotamersMoverLazyCreator.hh | |
| PDBReloadMover.cc | |
| PDBReloadMover.fwd.hh | PDBReloadMover forward declarations header |
| PDBReloadMover.hh | |
| PDBReloadMoverCreator.hh | |
| PeptideStapleMover.cc | Peptide Staples are covalent links between i/i+[4,7] residues in a helix. Applying a PeptideStapleMover creates one of these links |
| PeptideStapleMover.fwd.hh | |
| PeptideStapleMover.hh | Definition of classes for placing peptide staples in the pose |
| ProlineFixMover.cc | |
| ProlineFixMover.fwd.hh | |
| ProlineFixMover.hh | |
| PSSM2BfactorMover.cc | |
| PSSM2BfactorMover.fwd.hh | Switch the chain order |
| PSSM2BfactorMover.hh | |
| PSSM2BfactorMoverCreator.hh | |
| RepackSidechainsMover.cc | |
| RepackSidechainsMover.fwd.hh | |
| RepackSidechainsMover.hh | |
| RepackSidechainsMoverCreator.hh | |
| RepulsiveOnlyMover.cc | Calculate repulsive energy only for certain residues |
| RepulsiveOnlyMover.fwd.hh | |
| RepulsiveOnlyMover.hh | |
| ResidueTypeConstraintMover.cc | Assigns a ResidueTypeConstraint to a pose |
| ResidueTypeConstraintMover.fwd.hh | |
| ResidueTypeConstraintMover.hh | Assigns a ResidueTypeConstraint to a pose |
| ResidueTypeConstraintMoverCreator.hh | This class will create instances of protocols::moves::Mover ResidueTypeConstraintMover for the protocols::moves::MoverFactory |
| ResTypeFragmentMover.cc | |
| ResTypeFragmentMover.fwd.hh | |
| ResTypeFragmentMover.hh | |
| ReturnSidechainMover.cc | ReturnSidechainMover methods implemented |
| ReturnSidechainMover.fwd.hh | ReturnSidechainMover forward declarations header |
| ReturnSidechainMover.hh | Protocols::moves::Mover to "return" proper sidechains to a pose that was temporarily in centroid mode (can be used for any sidechain copying) |
| RingConformationMover.cc | Method definitions for RingConformationMover |
| RingConformationMover.fwd.hh | Forward declarations for RingConformationMover |
| RingConformationMover.hh | Declarations and simple accessor/mutator definitions for RingConformationMover |
| RotamerTrialsMinMover.cc | Protocols::moves::Mover for Rotamer-Trials with Minimization (based on RotamerTrialsMover) |
| RotamerTrialsMinMover.fwd.hh | |
| RotamerTrialsMinMover.hh | Wrapper mover for Rotamer-Trials with Minimization (based on RotamerTrialsMover) |
| RotamerTrialsMinMoverCreator.hh | This class will create instances of RotamerTrialsMinMover for the protocols::moves::MoverFactory |
| RotamerTrialsMover.cc | |
| RotamerTrialsMover.fwd.hh | |
| RotamerTrialsMover.hh | |
| RotamerTrialsMoverCreator.hh | This class will create instances of protocols::moves::Mover SidechainMCMover for the protocols::moves::MoverFactory |
| SaneMinMover.cc | |
| SaneMinMover.fwd.hh | |
| SaneMinMover.hh | |
| SaneMinMoverCreator.hh | |
| ScoreMover.cc | |
| ScoreMover.fwd.hh | ScoreMover forward declarations header |
| ScoreMover.hh | |
| ScoreMoverCreator.hh | |
| SequenceProfileMover.cc | Moverization of code that was embedded in the parser |
| SequenceProfileMover.fwd.hh | |
| SequenceProfileMover.hh | BS mover to get around a stupid "mover" that was embedded in the parser |
| SequenceProfileMoverCreator.hh | |
| SetReturningPackRotamersMover.cc | A pack mover which returns not just the best packer solution, but all nloop solutions |
| SetReturningPackRotamersMover.fwd.hh | |
| SetReturningPackRotamersMover.hh | A PackRotamers mover which returns a set of packed poses for when ndruns/nloop is in use |
| SetTorsion.cc | |
| SetTorsion.fwd.hh | |
| SetTorsion.hh | |
| SetTorsionCreator.hh | |
| ShakeStructureMover.cc | |
| ShakeStructureMover.fwd.hh | |
| ShakeStructureMover.hh | |
| SmoothFragmentMover.cc | |
| SmoothFragmentMover.fwd.hh | |
| SmoothFragmentMover.hh | |
| SuperimposeMover.cc | |
| SuperimposeMover.fwd.hh | SuperimposeMover forward declarations header |
| SuperimposeMover.hh | |
| SuperimposeMoverCreator.hh | |
| SwitchChainOrderMover.cc | |
| SwitchChainOrderMover.fwd.hh | Switch the chain order |
| SwitchChainOrderMover.hh | Switch the chain order |
| SwitchChainOrderMoverCreator.hh | |
| SwitchResidueTypeSetMover.cc | Switch between residue type sets (e.g. centroid and all atom) |
| SwitchResidueTypeSetMover.fwd.hh | Switch between residue type sets (e.g. centroid and all atom) |
| SwitchResidueTypeSetMover.hh | Switch between residue type sets (e.g. centroid and all atom) |
| SwitchResidueTypeSetMoverCreator.hh | |
| SymmetricFragmentMover.cc | |
| SymmetricFragmentMover.fwd.hh | |
| SymmetricFragmentMover.hh | |
| TailsScoreMover.cc | |
| TailsScoreMover.hh | |
| TaskAwareMinMover.cc | TaskAwareMinMover methods implemented |
| TaskAwareMinMover.fwd.hh | TaskAwareMinMover forward declarations header |
| TaskAwareMinMover.hh | MinMover which updates MoveMap to mirror PackerTask |
| TaskAwareMinMoverCreator.hh | |
| TorsionDOFMover.cc | TorsionDOFMover methods implemented |
| TorsionDOFMover.fwd.hh | TorsionDOFMover forward declarations header |
| TorsionDOFMover.hh | TorsionDOFMover header |
| Tumble.cc | Add constraints to the current pose conformation |
| Tumble.hh | Declaration of the MoverCreator class for the Tumble |
| TumbleCreator.hh | |
| VirtualRootMover.cc | Manipulate virtual roots on poses. This is a seperate mover mainly to be RosettaScriptable |
| VirtualRootMover.fwd.hh | VirtualRootMover forward declarations header |
| VirtualRootMover.hh | Manipulate virtual roots on poses |
| VirtualRootMoverCreator.hh | |
| WobbleMover.cc | |
| WobbleMover.hh | |
| ► sparta | |
| ANN.cc | |
| ANN.hh | |
| ChemicalShiftEvaluator.cc | |
| ChemicalShiftEvaluator.hh | |
| ChemicalShiftEvaluatorCreator.cc | |
| ChemicalShiftEvaluatorCreator.hh | |
| constants.hh | |
| GDB.cc | |
| GDB.hh | |
| main.cc | |
| PDB.cc | |
| PDB.hh | |
| Sparta.cc | |
| Sparta.hh | |
| SpartaUtil.cc | |
| SpartaUtil.hh | |
| util.cc | |
| util.hh | |
| ► ss_prediction | |
| SS_predictor.cc | |
| SS_predictor.fwd.hh | SS_predictor forward header |
| SS_predictor.hh | |
| ► star | |
| Extender.cc | |
| Extender.hh | |
| StarAbinitio.cc | |
| StarAbinitio.fwd.hh | |
| StarAbinitio.hh | |
| StarAbinitioMain.cc | |
| StarAbinitioMain.hh | |
| util.cc | |
| util.hh | |
| ► stepwise | |
| ► full_model_info | |
| FullModelInfoSetupFromCommandLine.cc | |
| FullModelInfoSetupFromCommandLine.fwd.hh | |
| FullModelInfoSetupFromCommandLine.hh | |
| ► monte_carlo | |
| ► mover | |
| AddMover.cc | |
| AddMover.fwd.hh | |
| AddMover.hh | |
| AddOrDeleteMover.cc | |
| AddOrDeleteMover.fwd.hh | |
| AddOrDeleteMover.hh | |
| DeleteMover.cc | |
| DeleteMover.fwd.hh | |
| DeleteMover.hh | |
| FromScratchMover.cc | |
| FromScratchMover.fwd.hh | |
| FromScratchMover.hh | |
| ResampleMover.cc | |
| ResampleMover.fwd.hh | |
| ResampleMover.hh | |
| TransientCutpointHandler.cc | |
| TransientCutpointHandler.fwd.hh | |
| TransientCutpointHandler.hh | |
| ► rna | |
| RNA_AddDeleteMonteCarlo.cc | |
| RNA_AddDeleteMonteCarlo.fwd.hh | |
| RNA_AddDeleteMonteCarlo.hh | |
| RNA_O2PrimeMover.cc | |
| RNA_O2PrimeMover.fwd.hh | |
| RNA_O2PrimeMover.hh | |
| RNA_TorsionMover.cc | |
| RNA_TorsionMover.fwd.hh | |
| RNA_TorsionMover.hh | |
| StepWiseMonteCarlo.cc | |
| StepWiseMonteCarlo.fwd.hh | |
| StepWiseMonteCarlo.hh | |
| StepWiseMonteCarloOptions.cc | |
| StepWiseMonteCarloOptions.fwd.hh | |
| StepWiseMonteCarloOptions.hh | |
| StepWiseMonteCarloUtil.cc | |
| StepWiseMonteCarloUtil.hh | |
| SWA_Move.cc | |
| SWA_Move.fwd.hh | |
| SWA_Move.hh | |
| SWA_MoveSelector.cc | |
| SWA_MoveSelector.fwd.hh | |
| SWA_MoveSelector.hh | |
| ► sampling | |
| ► general | |
| StepWiseClusterer.cc | |
| StepWiseClusterer.fwd.hh | |
| StepWiseClusterer.hh | |
| StepWiseClustererSilentBased.cc | |
| StepWiseClustererSilentBased.fwd.hh | |
| StepWiseClustererSilentBased.hh | |
| StepWisePoseAligner.cc | |
| StepWisePoseAligner.fwd.hh | |
| StepWisePoseAligner.hh | |
| ► legacy | |
| RigidBodySampler.cc | |
| RigidBodySampler.fwd.hh | |
| RigidBodySampler.hh | |
| ► protein | |
| ► beta | |
| StepWiseBetaAntiParallelJumpSampleGenerator.cc | |
| StepWiseBetaAntiParallelJumpSampleGenerator.hh | |
| ► checker | |
| ProteinAtrRepChecker.cc | |
| ProteinAtrRepChecker.fwd.hh | |
| ProteinAtrRepChecker.hh | |
| ► legacy | |
| StepWiseProteinMultiPosePacker.cc | |
| StepWiseProteinMultiPosePacker.fwd.hh | |
| StepWiseProteinMultiPosePacker.hh | |
| ► loop_close | |
| StepWiseProteinCCD_Closer.cc | |
| StepWiseProteinCCD_Closer.hh | |
| StepWiseProteinKIC_LoopBridger.cc | |
| StepWiseProteinKIC_LoopBridger.hh | |
| InputStreamWithResidueInfo.cc | |
| InputStreamWithResidueInfo.fwd.hh | |
| InputStreamWithResidueInfo.hh | |
| MainChainTorsionClasses.cc | |
| MainChainTorsionClasses.hh | |
| MainChainTorsionSet.cc | |
| MainChainTorsionSet.hh | |
| StepWisePoseSetup.cc | |
| StepWisePoseSetup.fwd.hh | |
| StepWisePoseSetup.hh | |
| StepWiseProteinBackboneSampler.cc | |
| StepWiseProteinBackboneSampler.hh | |
| StepWiseProteinJobParameters.cc | |
| StepWiseProteinJobParameters.fwd.hh | |
| StepWiseProteinJobParameters.hh | |
| StepWiseProteinJobParametersUtil.cc | |
| StepWiseProteinJobParametersUtil.fwd.hh | |
| StepWiseProteinJobParametersUtil.hh | |
| StepWiseProteinModeler.cc | |
| StepWiseProteinModeler.fwd.hh | |
| StepWiseProteinModeler.hh | |
| StepWiseProteinModelerOptions.cc | |
| StepWiseProteinModelerOptions.fwd.hh | |
| StepWiseProteinModelerOptions.hh | |
| StepWiseProteinPacker.cc | |
| StepWiseProteinPacker.fwd.hh | |
| StepWiseProteinPacker.hh | |
| StepWiseProteinPoseMinimizer.cc | |
| StepWiseProteinPoseMinimizer.fwd.hh | |
| StepWiseProteinPoseMinimizer.hh | |
| StepWiseProteinResidueSampler.cc | |
| StepWiseProteinResidueSampler.fwd.hh | |
| StepWiseProteinResidueSampler.hh | |
| StepWiseProteinScreener.cc | |
| StepWiseProteinUtil.cc | |
| StepWiseProteinUtil.hh | |
| ► rna | |
| ► bulge | |
| BulgeApplyMover.cc | |
| BulgeApplyMover.fwd.hh | |
| BulgeApplyMover.hh | |
| BulgeUnApplyMover.cc | |
| BulgeUnApplyMover.fwd.hh | |
| BulgeUnApplyMover.hh | |
| ► checker | |
| AtrRepChecker.cc | |
| AtrRepChecker.fwd.hh | |
| AtrRepChecker.hh | |
| ChainClosableGeometryChecker.cc | |
| ChainClosableGeometryChecker.fwd.hh | |
| ChainClosableGeometryChecker.hh | |
| ChainClosureChecker.cc | |
| ChainClosureChecker.fwd.hh | |
| ChainClosureChecker.hh | |
| RNA_BaseCentroidChecker.cc | |
| RNA_BaseCentroidChecker.fwd.hh | |
| RNA_BaseCentroidChecker.hh | |
| RNA_VDW_BinChecker.cc | Very fast version of VWD repulsion screening |
| RNA_VDW_BinChecker.fwd.hh | |
| RNA_VDW_BinChecker.hh | |
| ► connection | |
| StepWiseRNA_ConnectionSampler.cc | |
| StepWiseRNA_ConnectionSampler.fwd.hh | |
| StepWiseRNA_ConnectionSampler.hh | |
| ► helix | |
| RNA_HelixAssembler.cc | |
| RNA_HelixAssembler.fwd.hh | |
| RNA_HelixAssembler.hh | |
| ► legacy | |
| ► rigid_body | |
| StepWiseRNA_FloatingBaseSampler.cc | |
| StepWiseRNA_FloatingBaseSampler.fwd.hh | |
| StepWiseRNA_FloatingBaseSampler.hh | |
| StepWiseRNA_RigidBodyConnectionSampler.cc | |
| StepWiseRNA_RigidBodyConnectionSampler.hh | |
| StepWiseRNA_RigidBodySampler.cc | |
| StepWiseRNA_RigidBodySampler.fwd.hh | |
| StepWiseRNA_RigidBodySampler.hh | |
| ► suite | |
| StepWiseRNA_ClassicResidueSampler.cc | Sampler of a single residue, the heart of StepWise Assembly of RNA |
| StepWiseRNA_ClassicResidueSampler.fwd.hh | |
| StepWiseRNA_ClassicResidueSampler.hh | |
| StepWiseRNA_SuiteConnectionSampler.cc | Sampler of a single residue, the heart of StepWise Assembly of RNA |
| RNA_AnalyticLoopCloser.cc | |
| RNA_AnalyticLoopCloser.fwd.hh | |
| RNA_AnalyticLoopCloser.hh | |
| StepWiseRNA_JobParametersSetup.cc | |
| StepWiseRNA_JobParametersSetup.hh | |
| StepWiseRNA_PoseSetup.cc | |
| StepWiseRNA_PoseSetup.fwd.hh | |
| StepWiseRNA_PoseSetup.hh | |
| StepWiseRNA_PoseSetupFromCommandLine.cc | |
| StepWiseRNA_PoseSetupFromCommandLine.hh | |
| ► o2prime | |
| O2PrimePacker.cc | |
| O2PrimePacker.fwd.hh | |
| O2PrimePacker.hh | |
| ► phosphate | |
| MultiPhosphateSampler.cc | |
| MultiPhosphateSampler.fwd.hh | |
| MultiPhosphateSampler.hh | |
| PhosphateMove.cc | |
| PhosphateMove.fwd.hh | |
| PhosphateMove.hh | |
| PhosphateMover.cc | |
| PhosphateMover.fwd.hh | |
| PhosphateMover.hh | |
| PhosphateUtil.cc | |
| PhosphateUtil.hh | |
| ► rigid_body | |
| FloatingBaseClasses.hh | |
| StepWiseRNA_FloatingBaseSamplerUtil.cc | |
| StepWiseRNA_FloatingBaseSamplerUtil.hh | |
| ► sugar | |
| ► legacy | |
| StepWiseRNA_VirtualSugarJustInTimeInstantiatorOLD.cc | |
| StepWiseRNA_VirtualSugarJustInTimeInstantiatorOLD.fwd.hh | |
| StepWiseRNA_VirtualSugarJustInTimeInstantiatorOLD.hh | |
| StepWiseRNA_VirtualSugarJustInTimeInstantiator.cc | |
| StepWiseRNA_VirtualSugarJustInTimeInstantiator.fwd.hh | |
| StepWiseRNA_VirtualSugarJustInTimeInstantiator.hh | |
| StepWiseRNA_VirtualSugarSampler.cc | |
| StepWiseRNA_VirtualSugarSampler.hh | |
| StepWiseRNA_VirtualSugarSamplerFromStringList.cc | |
| StepWiseRNA_VirtualSugarSamplerFromStringList.fwd.hh | |
| StepWiseRNA_VirtualSugarSamplerFromStringList.hh | |
| StepWiseRNA_VirtualSugarUtil.cc | |
| StepWiseRNA_VirtualSugarUtil.fwd.hh | |
| StepWiseRNA_VirtualSugarUtil.hh | |
| SugarInstantiateMover.cc | |
| SugarInstantiateMover.fwd.hh | |
| SugarInstantiateMover.hh | |
| SugarModeling.cc | |
| SugarModeling.fwd.hh | |
| SugarModeling.hh | |
| SugarVirtualizeMover.cc | |
| SugarVirtualizeMover.fwd.hh | |
| SugarVirtualizeMover.hh | |
| StepWiseRNA_Classes.hh | |
| StepWiseRNA_Clusterer.cc | |
| StepWiseRNA_Clusterer.hh | |
| StepWiseRNA_CombineLongLoopFilterer.cc | |
| StepWiseRNA_CombineLongLoopFilterer.fwd.hh | |
| StepWiseRNA_CombineLongLoopFilterer.hh | |
| StepWiseRNA_JobParameters.cc | |
| StepWiseRNA_JobParameters.fwd.hh | |
| StepWiseRNA_JobParameters.hh | |
| StepWiseRNA_JobParametersUtil.cc | |
| StepWiseRNA_JobParametersUtil.fwd.hh | |
| StepWiseRNA_JobParametersUtil.hh | |
| StepWiseRNA_Minimizer.cc | |
| StepWiseRNA_Minimizer.fwd.hh | |
| StepWiseRNA_Minimizer.hh | |
| StepWiseRNA_Modeler.cc | |
| StepWiseRNA_Modeler.fwd.hh | |
| StepWiseRNA_Modeler.hh | |
| StepWiseRNA_ModelerOptions.cc | |
| StepWiseRNA_ModelerOptions.fwd.hh | |
| StepWiseRNA_ModelerOptions.hh | |
| StepWiseRNA_OutputData.cc | Output silent_file_data functions for Stepwise Assembly RNA |
| StepWiseRNA_OutputData.hh | |
| StepWiseRNA_PoseSelection.cc | |
| StepWiseRNA_PoseSelection.fwd.hh | |
| StepWiseRNA_PoseSelection.hh | |
| StepWiseRNA_ResidueInfo.cc | |
| StepWiseRNA_ResidueInfo.hh | |
| StepWiseRNA_ResidueSampler.cc | |
| StepWiseRNA_ResidueSampler.hh | |
| StepWiseRNA_Util.cc | |
| StepWiseRNA_Util.hh | |
| StepWiseModeler.cc | |
| StepWiseModeler.fwd.hh | |
| StepWiseModeler.hh | |
| ► screener | |
| AnchorSugarScreener.cc | |
| AnchorSugarScreener.fwd.hh | |
| AnchorSugarScreener.hh | |
| AtrRepScreener.cc | |
| AtrRepScreener.fwd.hh | |
| AtrRepScreener.hh | |
| BaseBinMapUpdater.cc | |
| BaseBinMapUpdater.fwd.hh | |
| BaseBinMapUpdater.hh | |
| BaseCentroidScreener.cc | |
| BaseCentroidScreener.fwd.hh | |
| BaseCentroidScreener.hh | |
| BulgeApplier.cc | |
| BulgeApplier.fwd.hh | |
| BulgeApplier.hh | |
| CentroidDistanceScreener.cc | |
| CentroidDistanceScreener.fwd.hh | |
| CentroidDistanceScreener.hh | |
| ChainClosableGeometryResidueBasedScreener.cc | |
| ChainClosableGeometryResidueBasedScreener.fwd.hh | |
| ChainClosableGeometryResidueBasedScreener.hh | |
| ChainClosableGeometryScreener.cc | |
| ChainClosableGeometryScreener.fwd.hh | |
| ChainClosableGeometryScreener.hh | |
| ChainClosableGeometryStubBasedScreener.cc | |
| ChainClosableGeometryStubBasedScreener.fwd.hh | |
| ChainClosableGeometryStubBasedScreener.hh | |
| ChainClosureScreener.cc | |
| ChainClosureScreener.fwd.hh | |
| ChainClosureScreener.hh | |
| FastForwardToNextResidueAlternative.cc | |
| FastForwardToNextResidueAlternative.fwd.hh | |
| FastForwardToNextResidueAlternative.hh | |
| FastForwardToNextRigidBody.cc | |
| FastForwardToNextRigidBody.fwd.hh | |
| FastForwardToNextRigidBody.hh | |
| IntegrationTestBreaker.cc | |
| IntegrationTestBreaker.fwd.hh | |
| IntegrationTestBreaker.hh | |
| NativeRMSD_Screener.cc | |
| NativeRMSD_Screener.fwd.hh | |
| NativeRMSD_Screener.hh | |
| O2PrimeScreener.cc | |
| O2PrimeScreener.fwd.hh | |
| O2PrimeScreener.hh | |
| PhosphateScreener.cc | |
| PhosphateScreener.fwd.hh | |
| PhosphateScreener.hh | |
| PoseSelectionScreener.cc | |
| PoseSelectionScreener.fwd.hh | |
| PoseSelectionScreener.hh | |
| ProteinAtrRepScreener.cc | |
| ProteinAtrRepScreener.fwd.hh | |
| ProteinAtrRepScreener.hh | |
| ProteinPackScreener.cc | |
| ProteinPackScreener.fwd.hh | |
| ProteinPackScreener.hh | |
| ResidueContactScreener.cc | |
| ResidueContactScreener.fwd.hh | |
| ResidueContactScreener.hh | |
| SampleApplier.cc | |
| SampleApplier.fwd.hh | |
| SampleApplier.hh | |
| SimplePoseSelection.cc | |
| SimplePoseSelection.fwd.hh | |
| SimplePoseSelection.hh | |
| SimpleRMSD_Screener.cc | |
| SimpleRMSD_Screener.fwd.hh | |
| SimpleRMSD_Screener.hh | |
| StepWiseResiduePairScreener.cc | |
| StepWiseResiduePairScreener.fwd.hh | |
| StepWiseResiduePairScreener.hh | |
| StepWiseScreener.cc | |
| StepWiseScreener.fwd.hh | |
| StepWiseScreener.hh | |
| StepWiseScreenerType.hh | |
| StepWiseScreenerUtil.cc | |
| StepWiseScreenerUtil.fwd.hh | |
| StepWiseScreenerUtil.hh | |
| StubApplier.cc | |
| StubApplier.fwd.hh | |
| StubApplier.hh | |
| StubDistanceScreener.cc | |
| StubDistanceScreener.fwd.hh | |
| StubDistanceScreener.hh | |
| SugarInstantiator.cc | |
| SugarInstantiator.fwd.hh | |
| SugarInstantiator.hh | |
| TagDefinition.cc | |
| TagDefinition.fwd.hh | |
| TagDefinition.hh | |
| VDW_BinScreener.cc | |
| VDW_BinScreener.fwd.hh | |
| VDW_BinScreener.hh | |
| StepWiseSampleAndScreen.cc | |
| StepWiseSampleAndScreen.fwd.hh | |
| StepWiseSampleAndScreen.hh | |
| StepWiseUtil.cc | |
| StepWiseUtil.hh | |
| ► surface_docking | |
| CentroidRelaxMover.cc | |
| CentroidRelaxMover.fwd.hh | |
| CentroidRelaxMover.hh | <add a="" description="" of="" the="" class>=""> |
| FullatomRelaxMover.cc | |
| FullatomRelaxMover.fwd.hh | |
| FullatomRelaxMover.hh | |
| SurfaceDockingProtocol.cc | |
| SurfaceDockingProtocol.fwd.hh | |
| SurfaceDockingProtocol.hh | |
| SurfaceOrientMover.cc | |
| SurfaceOrientMover.fwd.hh | |
| SurfaceOrientMover.hh | <add a="" description="" of="" the="" class>=""> |
| SurfaceParameters.cc | |
| SurfaceParameters.fwd.hh | |
| SurfaceParameters.hh | |
| SurfaceVectorFallbackConfiguration.cc | |
| SurfaceVectorFallbackConfiguration.fwd.hh | Forward header for OptionsSystemFallback class |
| SurfaceVectorFallbackConfiguration.hh | |
| SurfaceVectorFallbackConfigurationCreator.hh | |
| SurfaceVectorLoader.cc | |
| SurfaceVectorLoader.fwd.hh | |
| SurfaceVectorLoader.hh | |
| SurfaceVectorLoaderCreator.hh | |
| SurfaceVectorOptions.cc | |
| SurfaceVectorOptions.fwd.hh | SurfaceVectorOptions forward declarations header |
| SurfaceVectorOptions.hh | |
| SurfaceVectorOptionsCreator.hh | |
| ► symmetric_docking | |
| SymDockBaseProtocol.cc | |
| SymDockBaseProtocol.hh | |
| SymDockingHiRes.cc | |
| SymDockingHiRes.fwd.hh | |
| SymDockingHiRes.hh | |
| SymDockingLowRes.cc | |
| SymDockingLowRes.fwd.hh | |
| SymDockingLowRes.hh | |
| SymDockProtocol.cc | |
| SymDockProtocol.fwd.hh | |
| SymDockProtocol.hh | |
| SymDockProtocolCreator.hh | Declaration of the MoverCreator class for the SymDockProtocol |
| SymFoldandDockCreators.hh | |
| SymFoldandDockMoveRbJumpMover.cc | |
| SymFoldandDockMoveRbJumpMover.fwd.hh | |
| SymFoldandDockMoveRbJumpMover.hh | |
| SymFoldandDockRbTrialMover.cc | |
| SymFoldandDockRbTrialMover.fwd.hh | |
| SymFoldandDockRbTrialMover.hh | |
| SymFoldandDockSlideTrialMover.cc | |
| SymFoldandDockSlideTrialMover.fwd.hh | |
| SymFoldandDockSlideTrialMover.hh | |
| SymRestrictTaskForDocking.cc | When passed to a PackerTask, pack/design is limited to the protein interface |
| SymRestrictTaskForDocking.fwd.hh | |
| SymRestrictTaskForDocking.hh | When passed to a PackerTask, pack/design is limited to the interface |
| SymSidechainMinMover.cc | |
| SymSidechainMinMover.fwd.hh | |
| SymSidechainMinMover.hh | |
| ► toolbox | |
| ► match_enzdes_util | |
| AlignPoseToInvrotTreeMover.cc | |
| AlignPoseToInvrotTreeMover.fwd.hh | Forward declaration for inverse rotamer tree node base |
| AlignPoseToInvrotTreeMover.hh | Small class to setup an invrot tree in an existing pose |
| AllowedSeqposForGeomCst.cc | |
| AllowedSeqposForGeomCst.fwd.hh | Forward declaration for AllowedSeqposForGeomCst |
| AllowedSeqposForGeomCst.hh | |
| EnzConstraintIO.cc | |
| EnzConstraintIO.fwd.hh | |
| EnzConstraintIO.hh | |
| EnzConstraintParameters.cc | |
| EnzConstraintParameters.hh | |
| EnzCstTemplateRes.cc | |
| EnzCstTemplateRes.hh | |
| EnzdesCacheableObserver.cc | |
| EnzdesCacheableObserver.fwd.hh | |
| EnzdesCacheableObserver.hh | |
| EnzdesCstCache.cc | |
| EnzdesCstCache.fwd.hh | |
| EnzdesCstCache.hh | |
| EnzdesLoopsFile.cc | |
| EnzdesLoopsFile.fwd.hh | |
| EnzdesLoopsFile.hh | |
| EnzdesSeqRecoveryCache.cc | |
| EnzdesSeqRecoveryCache.fwd.hh | |
| EnzdesSeqRecoveryCache.hh | |
| ExternalGeomSampler.cc | |
| ExternalGeomSampler.fwd.hh | |
| ExternalGeomSampler.hh | |
| InvrotTarget.cc | |
| InvrotTarget.fwd.hh | Forward declaration for inverse rotamer target |
| InvrotTarget.hh | .hh file for inverse rotamer target |
| InvrotTree.cc | |
| InvrotTree.fwd.hh | Forward declaration for inverse rotamer tree node base |
| InvrotTree.hh | Class to hold inverse rotamers associated with theozyme / cstfile |
| InvrotTreeNode.cc | .cc file for inverse rotamer tree node |
| InvrotTreeNode.fwd.hh | Forward declaration for inverse rotamer target |
| InvrotTreeNode.hh | .hh file for inverse rotamer tree node |
| InvrotTreeNodeBase.cc | Forward declaration for inverse rotamer tree node base |
| InvrotTreeNodeBase.fwd.hh | Forward declaration for inverse rotamer tree node base |
| InvrotTreeNodeBase.hh | Forward declaration for inverse rotamer tree node base |
| LigandConformer.cc | Implementation for class to hold a ligand conformation |
| LigandConformer.fwd.hh | Forward declaration for a class to hold the geometry of a ligand conformation |
| LigandConformer.hh | Declaration of a class to hold a ligand conformation |
| MatchConstraintFileInfo.cc | |
| MatchConstraintFileInfo.fwd.hh | |
| MatchConstraintFileInfo.hh | |
| util_functions.cc | Bunch of utility functions |
| util_functions.hh | |
| ► pose_manipulation | |
| pose_manipulation.cc | |
| pose_manipulation.hh | Some general functions to manipulate poses. feel free to add your own |
| ► pose_metric_calculators | |
| BuriedUnsatisfiedPolarsCalculator.cc | |
| BuriedUnsatisfiedPolarsCalculator.hh | |
| CatPiCalculator.cc | |
| CatPiCalculator.hh | |
| ChargeCalculator.cc | |
| ChargeCalculator.hh | |
| ClashCountCalculator.cc | |
| ClashCountCalculator.hh | |
| DecomposeAndReweightEnergiesCalculator.cc | |
| DecomposeAndReweightEnergiesCalculator.hh | |
| ExplicitWaterUnsatisfiedPolarsCalculator.cc | |
| ExplicitWaterUnsatisfiedPolarsCalculator.hh | |
| FragQualCalculator.cc | |
| FragQualCalculator.hh | |
| HPatchCalculator.cc | |
| HPatchCalculator.hh | |
| InterGroupNeighborsCalculator.cc | |
| InterGroupNeighborsCalculator.fwd.hh | |
| InterGroupNeighborsCalculator.hh | |
| MetricValueGetter.cc | |
| MetricValueGetter.fwd.hh | |
| MetricValueGetter.hh | |
| NeighborhoodByDistanceCalculator.cc | |
| NeighborhoodByDistanceCalculator.fwd.hh | |
| NeighborhoodByDistanceCalculator.hh | |
| NeighborsByDistanceCalculator.cc | |
| NeighborsByDistanceCalculator.fwd.hh | |
| NeighborsByDistanceCalculator.hh | |
| NonlocalContactsCalculator.cc | |
| NonlocalContactsCalculator.hh | |
| NumberHBondsCalculator.cc | |
| NumberHBondsCalculator.hh | |
| PackstatCalculator.cc | |
| PackstatCalculator.hh | |
| PiPiCalculator.cc | |
| PiPiCalculator.hh | |
| ResidueDecompositionByChainCalculator.cc | |
| ResidueDecompositionByChainCalculator.hh | |
| ResidueDecompositionCalculator.cc | |
| ResidueDecompositionCalculator.hh | |
| RotamerBoltzCalculator.cc | |
| RotamerBoltzCalculator.fwd.hh | |
| RotamerBoltzCalculator.hh | |
| RotamerRecovery.cc | |
| RotamerRecovery.hh | Compare the rotamer recovery between a native protein and a list of other proteins |
| SaltBridgeCalculator.cc | |
| SaltBridgeCalculator.hh | |
| SemiExplicitWaterUnsatisfiedPolarsCalculator.cc | |
| SemiExplicitWaterUnsatisfiedPolarsCalculator.hh | |
| SequenceComparison.cc | |
| SequenceComparison.hh | |
| SurfaceCalculator.cc | |
| SurfaceCalculator.hh | |
| ► rotamer_set_operations | |
| RigidBodyMoveRotSetOps.cc | |
| RigidBodyMoveRotSetOps.fwd.hh | |
| RigidBodyMoveRotSetOps.hh | |
| SpecialRotamerRotSetOps.cc | |
| SpecialRotamerRotSetOps.fwd.hh | |
| SpecialRotamerRotSetOps.hh | |
| ► task_operations | |
| CrystalContactsOperation.cc | Exclude crystal contacts from design |
| CrystalContactsOperation.fwd.hh | Exclude crystal contacts from design |
| CrystalContactsOperation.hh | Exclude crystal contacts from design |
| CrystalContactsOperationCreator.hh | Exclude crystal contacts from design |
| DatabaseThread.cc | Picks a sequence from database by start and end position on the pose |
| DatabaseThread.fwd.hh | |
| DatabaseThread.hh | TaskOperation class that restricts a chain to repacking |
| DatabaseThreadCreator.hh | |
| DesignAroundOperation.cc | |
| DesignAroundOperation.fwd.hh | |
| DesignAroundOperation.hh | TaskOperation class that restricts a chain to repacking |
| DesignAroundOperationCreator.hh | |
| ImportUnboundRotamersOperation.cc | Import unbound (or native) rotamers into Rosetta! |
| ImportUnboundRotamersOperation.fwd.hh | |
| ImportUnboundRotamersOperation.hh | Rotamer set operation forward declaration |
| ImportUnboundRotamersOperationCreator.hh | |
| InterfaceTaskOperation.cc | Base class for TaskOperations that will work with docking to define an interface |
| InterfaceTaskOperation.fwd.hh | |
| InterfaceTaskOperation.hh | Base class for TaskOperations that will work with docking to define an interface |
| JointSequenceOperation.cc | Set designable residues to those observed in a set of structures |
| JointSequenceOperation.fwd.hh | |
| JointSequenceOperation.hh | Set every position to be designable to residues observed in a set of structures |
| JointSequenceOperationCreator.hh | |
| LayerOperations.cc | |
| LayerOperations.hh | |
| LayerOperationsCreator.hh | |
| LimitAromaChi2Operation.cc | Eliminate aromatic rotamers, of which chi2 are around 0, 180 degree. Chi2=0, 180 rotamers of aromatic residues ( PHE, TYR, HIS ) are not observed in nature very much, however Rosetta really like them. This is really pathology. For design purpose, we don't need them actually |
| LimitAromaChi2Operation.fwd.hh | |
| LimitAromaChi2Operation.hh | Rotamer set operation forward declaration |
| LimitAromaChi2OperationCreator.hh | |
| LinkResidues.cc | |
| LinkResidues.fwd.hh | |
| LinkResidues.hh | TaskOperation class that restricts a chain to repacking |
| LinkResiduesCreator.hh | |
| ModifyAnnealer.cc | Task operation to set high and low temps for annealer as well as whether or not to do a quench step |
| ModifyAnnealer.fwd.hh | Task operation to set high and low temps for annealer as well as whether or not to do a quench step |
| ModifyAnnealer.hh | Task operation to set high and low temps for annealer as well as whether or not to do a quench step |
| ModifyAnnealerCreator.hh | |
| PreventChainFromRepackingOperation.cc | |
| PreventChainFromRepackingOperation.fwd.hh | |
| PreventChainFromRepackingOperation.hh | TaskOperation class that restricts a chain to repacking |
| PreventChainFromRepackingOperationCreator.hh | |
| PreventResiduesFromRepackingOperation.cc | |
| PreventResiduesFromRepackingOperation.fwd.hh | |
| PreventResiduesFromRepackingOperation.hh | TaskOperation class that prevents a vector of residues indices from repacking parsed as a string that is comma delimited "," |
| PreventResiduesFromRepackingOperationCreator.hh | |
| ProteinCoreResFilter.cc | |
| ProteinCoreResFilter.hh | |
| ProteinCoreResFilterCreator.hh | |
| ProteinInterfaceDesignOperation.cc | |
| ProteinInterfaceDesignOperation.fwd.hh | |
| ProteinInterfaceDesignOperation.hh | TaskOperation class that restricts a chain to repacking |
| ProteinInterfaceDesignOperationCreator.hh | |
| ReadResfileFromDB.cc | |
| ReadResfileFromDB.fwd.hh | Forward declaration of the ReadResfileFromDB class |
| ReadResfileFromDB.hh | Read a refile indexed by the input structure tag from a supplied relational database |
| ReadResfileFromDBCreator.hh | |
| RestrictByCalculatorsOperation.cc | A class that applies arbitrary calculators (whose calculations return std::set< core::Size >) to restrict a PackerTask |
| RestrictByCalculatorsOperation.fwd.hh | A class that applies arbitrary calculators (whose calculations return std::set< core::Size >) to restrict a PackerTask |
| RestrictByCalculatorsOperation.hh | A class that applies arbitrary calculators (whose calculations return std::set< core::Size >) to restrict a PackerTask |
| RestrictByCalculatorsOperationCreator.hh | |
| RestrictChainToRepackingOperation.cc | |
| RestrictChainToRepackingOperation.fwd.hh | |
| RestrictChainToRepackingOperation.hh | TaskOperation class that restricts a chain to repacking |
| RestrictChainToRepackingOperationCreator.hh | |
| RestrictIdentitiesAtAlignedPositions.cc | |
| RestrictIdentitiesAtAlignedPositions.fwd.hh | |
| RestrictIdentitiesAtAlignedPositions.hh | |
| RestrictIdentitiesAtAlignedPositionsCreator.hh | |
| RestrictInterGroupVectorOperation.cc | |
| RestrictInterGroupVectorOperation.fwd.hh | |
| RestrictInterGroupVectorOperation.hh | Restricts design to only those residues between two groups of structures |
| RestrictInterGroupVectorOperationCreator.hh | |
| RestrictNativeResiduesOperation.cc | Restrict every residue in the current pose that is native to repacking. ie, only allow mutated positions to be designed |
| RestrictNativeResiduesOperation.fwd.hh | |
| RestrictNativeResiduesOperation.hh | Restrict every residue in the current pose that is native to repacking. ie, only allow mutated positions to be designed |
| RestrictNativeResiduesOperationCreator.hh | |
| RestrictNonSurfaceToRepackingOperation.cc | |
| RestrictNonSurfaceToRepackingOperation.fwd.hh | |
| RestrictNonSurfaceToRepackingOperation.hh | |
| RestrictNonSurfaceToRepackingOperationCreator.hh | |
| RestrictOperationsBase.cc | Base class for PoseMetricCalculator-using TaskOperations |
| RestrictOperationsBase.fwd.hh | Base class for PoseMetricCalculator-using TaskOperations |
| RestrictOperationsBase.hh | Base class for PoseMetricCalculator-using TaskOperations |
| RestrictResiduesToRepackingOperation.cc | |
| RestrictResiduesToRepackingOperation.fwd.hh | |
| RestrictResiduesToRepackingOperation.hh | TaskOperation class that restricts a vector of Size defined residues to repacking when parsed, it takes in a string and splits by "," |
| RestrictResiduesToRepackingOperationCreator.hh | |
| RestrictToAlignedSegments.cc | |
| RestrictToAlignedSegments.fwd.hh | |
| RestrictToAlignedSegments.hh | |
| RestrictToAlignedSegmentsCreator.hh | |
| RestrictToCDRH3Loop.cc | |
| RestrictToCDRH3Loop.fwd.hh | Forward declaration of the RestrictToCDRH3Loop class |
| RestrictToCDRH3Loop.hh | This class allows the selection for packing of the Antibody CDR-H3 loop by taking advantage of the PDB numbering schemes that are commonly used for Antibodies |
| RestrictToCDRH3LoopCreator.hh | |
| RestrictToInterface.cc | |
| RestrictToInterface.fwd.hh | |
| RestrictToInterface.hh | |
| RestrictToInterfaceCreator.hh | |
| RestrictToInterfaceOperation.cc | TaskOperation class that finds an interface and leaves it mobile in the PackerTask |
| RestrictToInterfaceOperation.fwd.hh | Forward declaration of a TaskOperation class that finds an interface leaves it mobile in the PackerTask |
| RestrictToInterfaceOperation.hh | TaskOperation class that finds an interface and makes it mobile in the PackerTask |
| RestrictToInterfaceOperationCreator.hh | |
| RestrictToInterfaceVectorOperation.cc | TaskOperation class that finds an interface based on: core/pack/task/operation/util/interface_vector_calculate.hh and leaves it mobile in the PackerTask |
| RestrictToInterfaceVectorOperation.fwd.hh | Forward declaration of a TaskOperation class that finds an interface leaves it mobile in the PackerTask |
| RestrictToInterfaceVectorOperation.hh | TaskOperation class that finds an interface based on InterfaceVectorDefinition and leaves it mobile in the PackerTask. Serves mostly to wrap InterfaceVectorDefinition into a TaskOperation. see src/core/pack/task/operation/util/interface_vector_calculate.hh |
| RestrictToInterfaceVectorOperationCreator.hh | |
| RestrictToLoopsAndNeighbors.cc | |
| RestrictToLoopsAndNeighbors.fwd.hh | Forward declaration of the RestrictToLoopsAndNeighbors class |
| RestrictToLoopsAndNeighbors.hh | This class allows the selection for packing (and possibly design) of residues contained in a Loops object as well as the neighbors within a specified cutoff distance, with the default and maximum cutoff at 10.0 A |
| RestrictToLoopsAndNeighborsCreator.hh | Creator class for the RestrictToLoopsAndNeighbors TaskOperation |
| RestrictToMoveMapChiOperation.cc | |
| RestrictToMoveMapChiOperation.fwd.hh | |
| RestrictToMoveMapChiOperation.hh | Makes it easier to use TF and MM in the same class |
| RestrictToMoveMapChiOperationCreator.hh | |
| RestrictToNeighborhoodOperation.cc | TaskOperation class that finds a neighborhood and leaves it mobile in the PackerTask |
| RestrictToNeighborhoodOperation.fwd.hh | Forward declaration of a TaskOperation class that finds a neighborhood; leaves it mobile in the PackerTask |
| RestrictToNeighborhoodOperation.hh | TaskOperation class that finds a neighborhood and makes it mobile in the PackerTask |
| RestrictToNeighborhoodOperationCreator.hh | |
| RestrictToTerminiOperation.cc | |
| RestrictToTerminiOperation.fwd.hh | Restrict to packing only the residues at either or both termini |
| RestrictToTerminiOperation.hh | |
| RestrictToTerminiOperationCreator.hh | |
| SelectByDensityFitOperation.cc | |
| SelectByDensityFitOperation.fwd.hh | |
| SelectByDensityFitOperation.hh | |
| SelectByDensityFitOperationCreator.hh | |
| SelectBySASAOperation.cc | |
| SelectBySASAOperation.fwd.hh | |
| SelectBySASAOperation.hh | |
| SelectBySASAOperationCreator.hh | |
| SelectResiduesWithinChain.cc | |
| SelectResiduesWithinChain.fwd.hh | |
| SelectResiduesWithinChain.hh | |
| SelectResiduesWithinChainCreator.hh | |
| SeqprofConsensusOperation.cc | Set designable residues to those observed in sequence profile |
| SeqprofConsensusOperation.fwd.hh | |
| SeqprofConsensusOperation.hh | |
| SeqprofConsensusOperationCreator.hh | |
| SetIGTypeOperation.cc | Task operation to set interaction graph type (linmem, lazy or double lazy) |
| SetIGTypeOperation.fwd.hh | Task operation to set Interaction graph Type |
| SetIGTypeOperation.hh | Task operation to set interaction graph type (linear memory, lazy or double lazy) |
| SetIGTypeOperationCreator.hh | |
| ThreadSequenceOperation.cc | |
| ThreadSequenceOperation.fwd.hh | |
| ThreadSequenceOperation.hh | TaskOperation class that restricts a chain to repacking |
| ThreadSequenceOperationCreator.hh | |
| AllowInsert.cc | |
| AllowInsert.fwd.hh | AllowInsert forward declarations header |
| AllowInsert.hh | |
| Cluster.cc | |
| Cluster.hh | |
| Cluster.impl.hh | Template implementation for clustering of silentstructs that are provided by iterators |
| DecoySetEvaluation.cc | |
| DecoySetEvaluation.fwd.hh | |
| DecoySetEvaluation.hh | |
| DecoySetEvaluation.impl.hh | |
| IGEdgeReweighters.cc | |
| IGEdgeReweighters.hh | |
| InteratomicVarianceMatrix.cc | |
| InteratomicVarianceMatrix.hh | |
| KCluster.cc | |
| KCluster.fwd.hh | |
| KCluster.hh | Fast clustering algorithm for large silent file |
| NetworkAlgorithms.cc | Calculate various network properties from poses |
| NetworkAlgorithms.fwd.hh | FOrward header for class that analyzes properties of residue networks |
| NetworkAlgorithms.hh | Computes network properties of a pose |
| PyReturnValuePolicyTest.hh | A few functions test how PyRosetta handle boost ReturnValuePolicy |
| SelectResiduesByLayer.cc | Select residues depending on layer: core, boundary, and surface The layer of residues are defined by accessible sufrace area of CB + mainchain |
| SelectResiduesByLayer.fwd.hh | |
| SelectResiduesByLayer.hh | Select residues depending on layer: core, boundary, and surface and the layer are defined by accessible sufrace area of each residue |
| superimpose.cc | |
| superimpose.hh | |
| ► topology_broker | |
| ► claims | |
| BBClaim.fwd.hh | |
| BBClaim.hh | |
| CutClaim.fwd.hh | |
| CutClaim.hh | |
| DofClaim.cc | |
| DofClaim.fwd.hh | |
| DofClaim.hh | |
| JumpClaim.fwd.hh | |
| JumpClaim.hh | |
| LegacyRootClaim.fwd.hh | |
| LegacyRootClaim.hh | |
| SequenceClaim.fwd.hh | |
| SequenceClaim.hh | |
| SymmetryClaim.fwd.hh | |
| SymmetryClaim.hh | |
| ► weights | |
| AbinitioMoverWeight.hh | |
| all.hh | |
| ConstAbinitioMoverWeight.hh | |
| LargeFragWeight.hh | |
| SmallFragWeight.hh | |
| SmoothFragWeight.hh | |
| AsymFoldandDockClaimer.cc | |
| AsymFoldandDockClaimer.fwd.hh | AsymFoldandDockClaimer forward declarations header |
| AsymFoldandDockClaimer.hh | |
| BasicJumpClaimer.cc | |
| BasicJumpClaimer.fwd.hh | The forward head for the BasicJumpClaimre |
| BasicJumpClaimer.hh | |
| ClaimerMessage.cc | |
| ClaimerMessage.fwd.hh | |
| ClaimerMessage.hh | |
| ConstraintClaimer.cc | |
| ConstraintClaimer.fwd.hh | |
| ConstraintClaimer.hh | |
| ConstraintEvaluatorWrapper.cc | |
| ConstraintEvaluatorWrapper.fwd.hh | |
| ConstraintEvaluatorWrapper.hh | |
| ConstraintEvaluatorWrapperCreator.cc | |
| ConstraintEvaluatorWrapperCreator.hh | |
| CoordConstraintClaimer.cc | |
| CoordConstraintClaimer.fwd.hh | |
| CoordConstraintClaimer.hh | |
| CutBiasClaimer.cc | |
| CutBiasClaimer.fwd.hh | |
| CutBiasClaimer.hh | |
| DensityScoringClaimer.cc | |
| DensityScoringClaimer.fwd.hh | |
| DensityScoringClaimer.hh | |
| DisulfJumpClaimer.cc | |
| DisulfJumpClaimer.fwd.hh | Protocols::topology_broker::DisulfJumpClaimer forward declarations header |
| DisulfJumpClaimer.hh | |
| Exceptions.hh | |
| FibrilModelingClaimer.cc | |
| FibrilModelingClaimer.fwd.hh | FibrilModelingClaimer forward declarations header |
| FibrilModelingClaimer.hh | |
| FoldandDockClaimer.cc | |
| FoldandDockClaimer.fwd.hh | FoldandDockClaimer forward declarations header |
| FoldandDockClaimer.hh | |
| FragmentClaimer.cc | |
| FragmentClaimer.fwd.hh | |
| FragmentClaimer.hh | |
| FragmentJumpClaimer.cc | |
| FragmentJumpClaimer.fwd.hh | |
| FragmentJumpClaimer.hh | |
| LoopFragmentClaimer.cc | |
| LoopFragmentClaimer.fwd.hh | |
| LoopFragmentClaimer.hh | |
| MembraneTopologyClaimer.cc | |
| MembraneTopologyClaimer.fwd.hh | |
| MembraneTopologyClaimer.hh | |
| MetalloClaimer.cc | |
| MetalloClaimer.fwd.hh | |
| MetalloClaimer.hh | |
| PcsEnergyController.cc | |
| PcsEnergyController.fwd.hh | |
| PcsEnergyController.hh | |
| PseudocontactShiftEnergyController.cc | |
| PseudocontactShiftEnergyController.fwd.hh | |
| PseudocontactShiftEnergyController.hh | |
| PseudocontactShiftEnergyController_Ts1.cc | |
| PseudocontactShiftEnergyController_Ts1.fwd.hh | |
| PseudocontactShiftEnergyController_Ts1.hh | |
| PseudocontactShiftEnergyController_Ts2.cc | |
| PseudocontactShiftEnergyController_Ts2.fwd.hh | |
| PseudocontactShiftEnergyController_Ts2.hh | |
| PseudocontactShiftEnergyController_Ts3.cc | |
| PseudocontactShiftEnergyController_Ts3.fwd.hh | |
| PseudocontactShiftEnergyController_Ts3.hh | |
| PseudocontactShiftEnergyController_Ts4.cc | |
| PseudocontactShiftEnergyController_Ts4.fwd.hh | |
| PseudocontactShiftEnergyController_Ts4.hh | |
| RigidChunkClaimer.cc | |
| RigidChunkClaimer.fwd.hh | |
| RigidChunkClaimer.hh | |
| SequenceClaimer.cc | |
| SequenceClaimer.fwd.hh | |
| SequenceClaimer.hh | |
| SequenceNumberResolver.cc | |
| SequenceNumberResolver.fwd.hh | |
| SequenceNumberResolver.hh | |
| StartStructClaimer.cc | |
| StartStructClaimer.fwd.hh | |
| StartStructClaimer.hh | |
| SymmetryClaimer.cc | |
| SymmetryClaimer.fwd.hh | SymmetryClaimer forward declaration header |
| SymmetryClaimer.hh | Basic Claimer for making Symmetry Claims |
| TemplateFragmentClaimer.cc | |
| TemplateFragmentClaimer.fwd.hh | |
| TemplateFragmentClaimer.hh | |
| TemplateJumpClaimer.cc | |
| TemplateJumpClaimer.fwd.hh | |
| TemplateJumpClaimer.hh | |
| TopologyBroker.cc | |
| TopologyBroker.fwd.hh | |
| TopologyBroker.hh | |
| TopologyClaimer.cc | |
| TopologyClaimer.fwd.hh | |
| TopologyClaimer.hh | |
| TopologyClaimerFactory.cc | |
| TopologyClaimerFactory.hh | |
| util.cc | |
| util.hh | |
| ► trajectory | |
| DbTrajectoryReader.cc | |
| DbTrajectoryReader.fwd.hh | |
| DbTrajectoryReader.hh | |
| DbTrajectoryWriter.cc | |
| DbTrajectoryWriter.fwd.hh | |
| DbTrajectoryWriter.hh | |
| ► unfolded_state_energy_calculator | |
| UnfoldedStateEnergyCalculatorJobDistributor.cc | |
| UnfoldedStateEnergyCalculatorJobDistributor.fwd.hh | |
| UnfoldedStateEnergyCalculatorJobDistributor.hh | |
| UnfoldedStateEnergyCalculatorMover.cc | |
| UnfoldedStateEnergyCalculatorMover.fwd.hh | |
| UnfoldedStateEnergyCalculatorMover.hh | |
| UnfoldedStateEnergyCalculatorMPIWorkPoolJobDistributor.cc | |
| UnfoldedStateEnergyCalculatorMPIWorkPoolJobDistributor.fwd.hh | |
| UnfoldedStateEnergyCalculatorMPIWorkPoolJobDistributor.hh | |
| UnfoldedStateEnergyCalculatorUtil.cc | |
| UnfoldedStateEnergyCalculatorUtil.hh | |
| ► viewer | |
| ConformationViewer.cc | |
| ConformationViewer.fwd.hh | |
| ConformationViewer.hh | |
| GraphicsState.hh | |
| marchingCubes.cc | |
| marchingCubes.hh | |
| SilentObserver.cc | |
| SilentObserver.fwd.hh | |
| SilentObserver.hh | |
| triangle.hh | |
| triangleIterator.cc | |
| triangleIterator.hh | |
| viewers.cc | |
| viewers.hh | |
| visualize.cc | |
| visualize.hh | |
| ► vip | |
| VIP_Mover.cc | Void Identification and Packing Mover. Identifies buried voids in an input structure and attempts to fill these using fixed backbone packing and the GOE energy |
| VIP_Mover.hh | |
| VIP_Report.cc | Prints information about changes implemented in vip mover |
| VIP_Report.hh | Class for reports from vip mover implementation |
| VIP_Utils.cc | Utility functions for VIP mover |
| VIP_Utils.hh | |
| ► wum | |
| DatabaseEntryWorkUnit.cc | A work unit that runs a database query, processes the results, and returns a string (presumably a database insert statement) |
| DatabaseEntryWorkUnit.fwd.hh | A work unit that runs a database query, processes the results, and returns a string (presumably a database insert statement) |
| DatabaseEntryWorkUnit.hh | |
| DatabaseQueryWorkUnitManager.hh | An MPI work unit manager that runs a given database query and creates a DatabaseEntryWorkUnit for each of the result rows. This class is templated such that the specific type of DatabaseEntryWorkUnit created is the template class |
| MoverList.cc | |
| MoverList.hh | |
| MPI_Relax.cc | |
| MPI_Relax.hh | |
| MPI_WorkUnitManager.cc | |
| MPI_WorkUnitManager.fwd.hh | |
| MPI_WorkUnitManager.hh | |
| MPI_WorkUnitManager_Slave.cc | |
| MPI_WorkUnitManager_Slave.hh | |
| SilentStructStore.cc | |
| SilentStructStore.fwd.hh | SilentStructStore class forward declarations header |
| SilentStructStore.hh | |
| WorkUnitBase.cc | |
| WorkUnitBase.fwd.hh | |
| WorkUnitBase.hh | |
| WorkUnitList.cc | |
| WorkUnitList.hh | |
| WorkUnitManager.cc | |
| WorkUnitManager.fwd.hh | |
| WorkUnitManager.hh | |
| ► wum2 | |
| EndPoint.cc | Non MPI version of EndPoint |
| EndPoint.fwd.hh | Non MPI version of EndPoint This class is required because SingleNode role needs to use an EndPoint that is not MPI dependent (ie just a wrapper for 2 queues) |
| EndPoint.hh | Non-MPI version of EndPoint |
| MPI_EndPoint.cc | Handles communication between different roles in mpi |
| MPI_EndPoint.fwd.hh | Handles communication between different roles in mpi |
| MPI_EndPoint.hh | Handles communication between different roles in mpi |
| WorkUnit.cc | |
| WorkUnit.fwd.hh | Foward decls for base work unit (abstract) for wum2 and some commonly used derived work units |
| WorkUnit.hh | |
| WUQueue.cc | |
| WUQueue.fwd.hh | Foward decls for WUQueue, deque of WU with memory tracking |
| WUQueue.hh | Deque of WU with memory tracking |
| WUQueueBuffer.cc | Foward decls for WUQueueBuffer, memory aware structure that links irecv and isend with their mpi::request status, so buffers are maintained until messages are sent/recvd |
| WUQueueBuffer.fwd.hh | Foward decls for WUQueueBuffer, memory aware structure that links irecv and isend with their mpi::request status, so buffers are maintained until messages are sent/recvd |
| WUQueueBuffer.hh | Memory aware structure that links irecv and isend with their mpi::request status, so buffers are maintained until messages are sent/recvd |
1.8.7